Methods for inhibiting the binding of endosialin to ligands

ABSTRACT

The invention provides methods for inhibiting the interaction of endosialin with endosialin ligands. The inhibition is effectuated on the genetic level, by inhibiting endosialin gene expression, and on the protein level, by blocking the interaction of cell-surface expressed endosialin with ligands such as fibronectin and collagen. The invention provides methods for identifying inhibitors of the interaction of endosialin with endosialin ligands. Also provided are methods for inhibiting angiogenesis and neovascularization in vivo and in vitro.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.12/062,630, filed Apr. 4, 2008, now U.S. Pat. No. 7,807,382, whichclaims the benefit of U.S. Provisional Application No. 60/910,362, filedApr. 5, 2007, and of U.S. Provisional Application No. 60/980,026, filedOct. 15, 2007. This application incorporates by reference each of U.S.application Ser. No. 12/062,630, U.S. Application No. 60/910,362, andU.S. Application No. 60/980,026.

FIELD

The invention relates generally to the field of immunotherapeutics. Morespecifically, the invention relates to compositions and methods for thedisruption of endosialin interaction with its substrates to inhibitcellular functions, including angiogenesis and cell motility.

BACKGROUND

Various publications, including patents, published applications,technical articles and scholarly articles are cited throughout thespecification. Each of these cited publications is incorporated byreference herein, in its entirety and for all purposes.

Angiogenesis is a regulated process involving the formation of new bloodvessels. It plays an essential role in normal growth, embryonicdevelopment, wound healing, and other physiological processes(Yancopoulos et al. (2000) Nature, 407:242-8). Within the developingcapillary, extracellular matrix (ECM) proteins serve as a structuralscaffold for proliferating endothelial and tumor tissues and providesupport for the growth of tumor cells. De novo angiogenesis is involvedin several disease states including cancer, where the formation of new“embryonic-like” blood vessels (referred to as neovascularizationherein) appear that differ from normal vasculature with regards tostructure and function (Hanahan et al. (2000) Cell, 100:57-70). A numberof in vivo and in vitro studies have demonstrated biological differencesbetween normal and disease-associated vasculature using various modelsystems of angiogenesis, thereby raising the possibility of novelanti-angiogenic compounds that can selectively inhibit vessel formationof the embryonic-type, tumor-associated endothelial cells for therapy ofneovascular disease. In light of these opportunities for therapy, anintense search for potential targets that can specifically inhibit tumorand other neovascular disease-associated endothelial or stromal(fibroblasts, pericytes, etc.) cell growth and function is ongoing.

In an attempt to identify such targets, strategies have been designed toidentify cell surface antigens of tumor stroma as well as isolatespecific proteins or RNA that are expressed in tumor stromal cells(Rettig et al. (1992) Proc. Natl. Acad. Sci. USA, 89:10832-6; St. Croixet al. (2000) Science, 289:1197-1202). These strategies have identifieda cell surface protein that appears to be specifically expressed intumor stromal cells referred to as endosialin (or tumor endothelialmarker 1 (TEM1) or CD248).

Examination of gene expression patterns in normal and neoplastic tissueindicates upregulation of endosialin mRNA expression in tumorneovessels. (St Croix et al. (2000) Science, 289:1197-1202). Similarendosialin expression levels were noted in human colorectal cancer(Rmali et al. (2005) World J. Gastroenterol., 11:1283-1286), breastcancer tissues (Davies et al. (2004) Clin. Exp. Metastasis, 21:31-37),and histiocytomas (Dolznig et al. (2005) Cancer Immun., 5:10). Humanendosialin expression has been observed in highly invasive glioblastoma,anaplastic astrocytomas, and metastatic carcinomas, including melanomas(Brady et al. (2004) J. Neuropathol. Exp. Neurol., 63:1274-1283; Huberet al. (2006) J. Cutan. Pathol., 33:145-155).

The use of antibodies in immunohistochemistry studies have found robustexpression of endosialin in a number of neovascular endothelial cells,fibroblasts and/or pericytes (Virgintino et al. (2007) Angiogenesis,10:35-45) in malignant tissues, while expression in cell lines derivedfrom embryonic-like endothelial cultures such as but not limited toHUVEC (Human Umbilical Vein Endothelial Cells) or HMVEC-(Neonatal DermalMicrovascular Endothelial Cells) is limited. Analysis of antibodies,polypeptides or non-protein ligands that can bind to endosialin haveidentified a subset of such molecules that can suppress the ability ofendosialin to bind to its substrate and/or suppress intracellularactivities leading to cell stasis or death.

Rettig et al. described monoclonal antibodies that recognize antigens onvessels within various cancer types (Rettig et al. (1992) Proc. Natl.Acad. Sci. USA, 89:10832-6). One of these was designated FB5 and wasgenerated through immunization of mice with human embryonic fibroblasts.FB5 recognizes a ˜100 kDa protein on the surface of a neuroblastoma cellline, LA1-5s (U.S. Pat. No. 5,342,757). FB5 is a murine antibody (IgG1)that binds to endosialin and has been shown to recognize endothelialcells associated with a variety of different cancer types. Structuralevaluation has classified endosialin as a C-type lectin-like, integralmembrane protein, comprised of five globular extracellular domains(including a C-type lectin domain, one domain with similarity to theSushi/ccp/scr pattern, and three EGF repeats). The protein also containsa mucin-like region, a transmembrane segment, and a short cytoplasmictail. The protein appears to be a glycoprotein. Carbohydrate analysisshows that the endosialin core protein has an abundance of O-linkedglycosylation (Christian et al. (2001) J. Biol. Chem., 276:48588-48595).Subsequent work combined the complementarity determining regions (CDRs)of the mouse FB5 into a human IgG1 backbone to create a humanizedantibody that binds to vessels within malignant tissues as well as asubset of cells in HMVEC cultures.

Tem1 knockout mice develop normally and exhibit normal wound healing,suggesting that endosialin is not required for neovascularization duringfetal development or wound repair. (Nanda et al. (2006) Proc. Natl.Acad. Sci. USA, 103:3351-3356). When colorectal cancer cells wereimplanted in the abdominal sites of Tem1 knockout mice, however, theloss of endosialin expression correlated with a reduction in tumorgrowth, invasion, and metastases as compared to parental animals. Theabsence of endosialin expression has been shown to reduce growth,invasion, and metastasis of human tumor xenografts in an endosialinknockout mouse. (Nanda et al. (2006) Proc. Natl. Acad. Sci. USA,103:3351-3356). Additionally, lack of endosialin led to an increase insmall immature blood vessels and decreased numbers of medium and largetumor vessels.

Neovascularization is associated with a number of disease states. Incancer it is believed that neovascularization is important to supplytumors with blood. In non-oncology cancer or malignant diseases such asretinopathy and macular degeneration, uncontrolled neovascularizationcauses loss of sight (Wilkinson-Berka (2004) Curr. Pharm. Des.,10:3331-48; Das and McGuire (2003) Prog. Retin. Eye Res., 22:721-48).Moreover, several reports have identified a role of neovascularizationin inflammatory disease (Paleolog and Miotla (1998) Angiogenesis,2(4):295-307). Methods to better understand molecular pathways inembryonic-like endothelial and precursor cells as well asendothelial-associated cells (pericytes, fibroblasts, etc.) associatedwith these disease states will lead to the development of novel drugs totreat these diseases. Conversely, neovascularization is associated withwound healing (Galiano et al. (2004) Am. J. Pathol., 164:1935-47).Identification of molecular pathways that promote vascularization forwound healing can offer the ability to identify drugs and factors thatcan promote these processes for enhancing wound treatment associatedwith trauma, burns and infection.

A difficult problem in effective antiangiogenic and proangiogenictherapy is the nondefined nature of biological processes of moleculesand associated pathways that are important for activating cellularprocesses associated with neovascularization (Bagley et al. (2003)Cancer Res., 63:5866-73). The ability to identify and elucidatemolecules and their function in regulating a given pathway can lead tothe isolation of effective compounds that have stimulatory or inhibitoryactivity in neovascular-associated diseases such as cancer,inflammation, ocular disease, cardiovascular disease, and wound healing.The ability to isolate and study these compounds via molecular-basedassays would provide further utility for evaluating their effects tospecifically suppress or stimulate the normal biology of cells involvedin neovascularization in contrast to adult-like endothelial cellsassociated with vessels in normal adult tissue (Asahara and Kawamoto(2004) Am. J. Physiol. Cell Physiol., 287:C572-9).

SUMMARY

The invention features methods for inhibiting the interaction of anendosialin-expressing cell with a ligand for endosialin.

In one aspect, the methods comprise inhibiting expression of endosialinin an endosialin-expressing cell at the genetic level. Ligands forendosialin can be extracellular matrix proteins such as collagen orfibronectin. In some embodiments, the ligand is collagen I or collagenIV. In preferred embodiments, the cell is a mammalian cell. Regulationof endosialin expression at the genetic level can be effectuated by anymeans suitable in the art, such as antisense nucleic acid molecule,double stranded RNA, ribozymes, hammerhead ribozymes, decoyoligonucleotides, and the like. Regulation of endosialin expression canalso be accomplished by knocking out the gene encoding endosialin.

In another aspect, the methods comprise physically obstructingendosialin expressed on the surface of an endosialin expressing cell,thereby inhibiting the interaction of the cell with an endosialinligand. Ligands for endosialin can be extracellular matrix proteins suchas collagen (e.g., collagen I or collagen IV) or fibronectin.

Obstruction of cell surface endosialin can be effectuated by any meanssuitable in the art, such as small molecule inhibitors, polypeptideinhibitors, antibodies that specifically bind to endosialin, antibodiesthat specifically bind to an endosialin ligand, and the like. In someembodiments, competitive inhibitors are employed to inhibit theinteraction of endosialin or an endosialin-expressing cell with a ligandfor endosialin. In some embodiments, the competitive inhibitors may beendosialin ligands, endosialin-binding fragments of endosialin ligands,for example, endosialin-binding fragments of collagen or fibronectin.Preferred competitive inhibitors are endosialin-binding fragments ofcollagen I, collagen IV, or fibronectin. Most preferred competitiveinhibitors are the 70 kDa N-terminal fragment of fibronectin, the 45 kDagelatin binding fragment of fibronectin, and the 30 kDa heparin bindingfragment of fibronectin.

Suitable antibodies can be chimeric antibodies, humanized antibodies,fully human antibodies, antigen-binding fragments that specifically bindantigen, and the like. In some embodiments, the affinity of antibody forantigen is preferably less than about 1×10⁻⁷ M, more preferably lessthan about 1×10⁻⁸ M, even more preferably less than about 1×10⁻⁹ M, andmost preferably less than about 1×10⁻¹⁰ M. In some preferredembodiments, the antibody is an anti-endosialin antibody or anantigen-binding fragment that specifically recognizes endosialin. Insome embodiments, the antibody or antigen-binding fragment comprises aheavy chain comprising CDR1, CDR2, and CDR3 of SEQ ID NO:28, 30, and 32,respectively, and a light chain comprising CDR1, CDR2, and CDR3 of SEQID NO: 13, 15, and 17, respectively. In some embodiments, the antibodiesor antigen-binding fragments can comprise a heavy chain comprising avariable domain of SEQ ID NO: 34 and a light chain comprising a variabledomain of SEQ ID NO: 19. In some embodiments, the antibodies orantigen-binding fragments can comprise a heavy chain comprising theamino acid sequence of SEQ ID NO:22 or 26 and a light chain comprisingthe amino acid sequence of SEQ ID NO:11. Antibodies M4 and M4.1 arehumanized antibodies to human endosialin. While antibodies M4 and M4.1share a light chain sequence, they differ in their heavy chain by asingle amino acid sequence shown, for example, at residue 429 of SEQ IDNO:20 relative to residue 429 of SEQ ID NO:24. The amino acid change isthe result of a single nucleotide alteration shown, for example, atnucleotide 1286 of SEQ ID NO: 19 relative to nucleotide 1286 of SEQ IDNO:23. In some embodiments, the antibodies that can be used inaccordance with the invention are produced by cells having ATCC Access.No. PTA-7554 or ATCC Access. No. PTA-9017.

Inhibition of endosialin interaction with ligands for endosialin canaffect pathways, cascades, and downstream effects brought about by thenormal interaction. For example, obstructing or inhibiting theinteraction of an endosialin-expressing cell with an endosialin ligandcan inhibit the activation of integrins, the activation of matrixmetalloproteases, and/or the expression of matrix metalloproteases. Cellmotility can be inhibited. Most preferably, angiogenesis orneovascularization is inhibited.

In some embodiments, inhibition of the interaction of theendosialin-expressing cell with its ligand inhibits the activation ofintegrin β1, β2, or β3. In some embodiments, inhibition of theinteraction of the endosialin-expressing cell with its ligand inhibitsmigration of the cell. In some embodiments, inhibition of theinteraction of the endosialin-expressing cell with its ligand inhibitsthe activation or expression of a matrix metalloprotease. In preferredembodiments, the matrix metalloprotease is MMP-9.

The invention also features methods for inhibiting angiogenesis orneovascularization. The methods include in vitro and in vivo inhibitionof angiogenesis or neovascularization. In some aspects, the methodscomprise administering to a subject a therapeutically effective amountof an antibody or antigen-binding fragment that specifically bindsendosialin or composition that obstructs endosialin expressed on thesurface of a cell such that the interaction of the cell with anendosialin ligand is inhibited. This inhibition suppresses angiogenesisand/or neovascularization of a tissue, organ, or neoplasm in the subjectto which the composition is administered. Ligands for endosialin can beextracellular matrix proteins such as collagen (e.g., collagen I orcollagen IV) or fibronectin. The composition can comprise any molecule,such as those described and exemplified herein, that can physicallyobstruct the interaction of cell surface endosialin with at least oneendosialin ligand. Examples of such molecules include, withoutlimitation, small molecule inhibitors, polypeptide inhibitors,antibodies that specifically bind to endosialin, antibodies thatspecifically bind to an endosialin ligand, antigen-binding fragments,and the like. Suitable antibodies can be chimeric antibodies, humanizedantibodies, fully human antibodies, antibody fragments, and the like.

Also featured are assays and methods for identifying agents that enhance(“agonists”) or reduce (“antagonists”) the interaction of endosialinwith an endosialin ligand. In one aspect of methods for identifying suchantagonists, the methods comprise contacting endosialin with a testcompound, thereby forming an endosialin-test compound complex,contacting the endosialin-test compound complex with a ligand forendosialin, and quantifiably measuring the interaction of endosialinwith the ligand in the presence and in the absence of the test compound,wherein a decrease in the level of interaction of endosialin with theligand in the presence of the test compound indicates that the testcompound is an antagonist of the interaction of endosialin with theligand. In one embodiment, the methods for identifying agonists orantagonists of the interaction of endosialin with a ligand forendosialin comprises contacting endosialin with a ligand for endosialinin the presence and absence of a test compound and quantifiablymeasuring the interaction of endosialin with the ligand, wherein anincrease or a decrease in the level of interaction of endosialin withthe ligand in the presence of the test compound indicates that the testcompound is an agonist or antagonist, respectively, of the interactionof endosialin with the ligand. In the inventive assays, the endosialincan be bound to a cell membrane, a cell membrane fragment, an artificiallipid bilayer, or a solid support. In some aspects, the ligand can bebound to a solid support. Ligands for endosialin can be extracellularmatrix proteins such as collagen or fibronectin.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B show immunohistochemical analysis of endosialin-positivecells of malignant tissue. Tumors were isolated from patients withcolorectal cancer and flash frozen in liquid nitrogen. Samples werethin-sectioned and stained with anti-endosialin or isotype controlantibody. As shown, vessels in the tumor (FIG. 1A) stained positive forendosialin while isotype control antibody stained serial section wasnegative (FIG. 1B).

FIGS. 2A and 2B show immunohistochemical analysis of endosialin-positivecells of normal tissue. Normal tissues were isolated from patients bybiopsy and flash frozen in liquid nitrogen. Samples were thin-sectionedand stained with anti-endosialin or isotype control antibody. As shown,normal tissue contained few EPCs (arrow, FIG. 2A) while isotype controlantibody stained serial section were negative (FIG. 2B). Many normaltissues tested had a few EPCs as determined by in situ or antibodystaining.

FIG. 3 shows isolation of endosialin-positive cells from primaryendothelial cultures. HMVEC cultures were enriched for EPCs by panningEndosialin-panned cultures were then compared to HMVEC parental culturesfor percentage of endosialin-expressing cells. As shown, the pannedculture had a much higher number of endosialin-positive cells ascompared to the non-panned parental culture as determined byimmunostaining via anti-endosialin antibody followed by a fluorescentconjugated secondary antibody. Cell number of each field was determinedby light microscopy.

FIG. 4 shows that recombinant endosialin (Fc-TEM1) binds toextracellular matrix proteins (EMPs). ELISA plates, precoated with EMPfibronectin (FN), collagen (COL; including collagen type I (COLI) andcollagen type IV (COL IV)), vitronectin (VN), laminin (LN), or gelatin(Gel), were blocked with ELISA assay buffer prior to addition ofpurified Fc-TEM1 protein at increasing concentrations. Following a twohour incubation, the plates were washed and assayed for binding using aHRP-linked goat-anti-mouse secondary mAb specific for the Fc tail usingstandard ELISA conditions. Plates were washed and developed and thenassayed using a plate reader at OD 450 nm. As shown in FIG. 4A, theFc-TEM1 bound to FN and COL robustly while weak binding was observedwith LM, VN, or Gel. For FIG. 4B, an ELISA plate was pre-coatedovernight with the following antigens: Staphylococcus enterotoxin B(STEB), ovalbumin (OVA), bovine gamma globulin (BGG), tumor-associated90-kD glycoprotein antigen expressed on most melanoma cells (TA90), henegg lysozyme (HEL), tetanus toxoid (TT), 1% BSA, human mesothelin, humanGM-CSF, goat IgG, and mouse IgG. Fc-TEM1 was added at increasing amounts(5, 10, 50 ug/ml) and allowed to adhere for 2 hours. Plates were thenwashed and HRP-conjugated goat-anti-mouse antibody was added to detectbound Fc-TEM1.

FIG. 5 shows mapping of fibronectin (FN) binding domains to endosialin.Proteolytic and recombinant fragments derived from fibronectin (FN) wereassessed for the ability to support TEM-1 binding. FN fragmentsevaluated include: the N-terminal 70 kDa fragment (Sigma Cat. No. F0287)(obtained by cathepsin D digestion of fibronectin); the 30 kDa heparinbinding fragment (Sigma Cat. No. F9911); the 45 kDa gelatin bindingfragment (Sigma Cat. No. F0162) (both obtained from trypsin digestion ofthe 70 kDa fragment); the 120 kDa fragment containing the cellattachment domain (“the 120 kDa fragment”); and two recombinantfragments: Fn2, which contains the first 7 FN type III domains, and Fn4,which contains the site of interchain disulfide bonds and α4β1 integrinbinding domain. The diagram of FN structure was adapted fromWierzbicka-Patynowski et al. (2003) J. Cell Sci., 116:3269-76.

FIG. 6 shows recombinant Fc-TEM1 binding to EMP and fibronectin in thepresence of inhibitors. M4 is a humanized antibody to human endosialin,while rbtTEM1 is a rabbit antibody to human endosialin. The assay wasperformed as described in FIG. 4, except that antibodies were added tomeasure the ability to perturb or block Fc-TEM1 to bind to FN. As shownin this figure, M4 was able to inhibit Fc-TEM1 binding to FN while anon-specific control (HuIgG) was not.

FIG. 7 shows endosialin binding to EMP fragments and inhibition thereofby endosialin-EMP inhibitor compounds. The fibronectin fragments areillustrated in FIG. 5. FIG. 7A shows binding to protein fragmentsderived from native FN. FIG. 7B shows binding to protein fragmentsderived from denatured FN. For FIGS. 7A and 7B, FN fragment was coatedon an ELISA plate at the indicated concentrations. An anti-FN polyclonalantibody followed by addition of HRP-conjugated goat-anti-rabbitsecondary antibody was used to detect intact bound proteins. Fc-TEM1(1.25 ug/ml) was added and allowed to bind for 2 hours. Plates were thenwashed and HRP-conjugated goat-anti-mouse antibody was added to detectbound Fc-TEM1. The hatched bar (Fc-TEM1-native) in FIG. 7B representsFc-TEM1 binding to nondenatured FN. As shown, endosialin binds to theN-terminal region of fibronectin, as little or no binding was detectedfor binding to fragments FN-2, FN-4, or 120 kDa. Polyclonal antibodiesto fibronectin bound to all fragments. FIGS. 7C and 7D show binding ofFc-TEM1 to the 70 kDa fragment of FN and inhibition of the interactionby endosialin-EMP inhibitor compounds. Whole FN and the 70 kDa FNprotein were coated onto an ELISA plate at a fixed concentration of ˜15nmol/well for both proteins. Fc-TEM1 (1.25 ug/ml) was preincubated at 4°C. for 1 hour with increasing amounts of anti-endosialin antibody M4 orisotype control IgG. Fc-TEM1/M4 (FIG. 7C) or Fc-TEM1/IgG (FIG. 7D)complexes were added to FN- and 70 kDa-coated wells and incubated for 2hours at room temperature. Bound Fc-TEM1 protein was detected by theaddition of HRP-conjugated goat-anti-mouse secondary antibody.

FIG. 8 illustrates a change in cell morphology on a gelatinous proteinmixture sold under the trade name MATRIGEL (BD Biosciences) uponexpression of endosialin. 8E4 cells of either CHO-K1 or CHO-TEM1 wereseeded onto a 96-well-plate coated with MATRIGEL and incubated at 37° C.Following overnight incubation, the cells were photographed formacroscopic examination of tubule formation.

FIG. 9 shows endosialin-mediated cellular binding to EMP fragments. CHOcells were transfected with a vector expressing endosialin or mock cDNA.Cells were confirmed to express cell surface endosialin (CHOTEM1) whilethose transfected with mock (CHOK1) did not. For FIG. 9A, ChineseHamster Ovary (CHO) cells were added to a pre-coated 96-well platecontaining various ECM proteins. The cells were allowed to adhere for 1hour at 37° C. and wells were washed extensively to remove any looselybound cells. The number of attached cells was determined using theCELLTITER-GLO Luminescent Cell Viability Assay. Abbreviations: Col,Collagen; FN, fibronectin; LN, laminin; TN, tenascin; VN, vitronectin;Neg, bovine serum albumin. For FIG. 9B, Chinese Hamster Ovary (CHO)cells were transfected with a vector expressing endosialin or mock cDNA.Cells were confirmed by FACS analysis to express cell surface endosialin(CHOTEM1) while those transfected with mock (CHOK1) did not. Cells werethen tested for the ability to bind EMP fibronectin alone or incombination with anti-endosialin antibody M4 or control IgG. FIG. 9Bdemonstrates that anti-endosialin antibody M4 reducesendosialin-mediated cell adhesion to FN. Cells (1.5E5) were preincubatedfor 1 hour at 4° C. with antibody M4 (100 ug/ml) or an IgG isotypecontrol antibody (100 ug/ml). For FIG. 9C, cells were tested for theability to bind full length FN or fibronectin fragments. As shown inFIG. 9A, the number of adherent CHO-TEM1 cells was 6-fold higher thanthe number of parental CHO-K1 cells in wells coated with FN. Nosignificant differences in adhesion between CHO-K1 and CHO-TEM1 onsurfaces coated with laminin or vitronectin were observed, whileadhesion to collagens and tenascin was too weak to assess any valuabledifferences (FIG. 9A). Pretreatment of CHO-TEM1 cells with M4 antibodyresulted in 50% reduction of TEM1-FN-dependent cell adhesion, while IgGcontrol antibody had no effect (FIG. 9B). M4 antibody treatment did notaffect FN-dependent, endosialin-independent cell adhesion (baselineadhesion) of parental CHO-K1 cells. CHO-TEM1 cells showed a 3- to 5-foldincreased adhesion to FN, 70 kDa, and 30 kDa fragments compared toparental CHO-K1 cells, whereas no significant adhesion was seen to 45kDa or Fn2 fragments. CHO-TEM1 cells bound MATRIGEL five times betterthan CHO-K1 (FIG. 9C).

FIG. 10 shows identification of endosialin-EMP collagen inhibitorcompounds. CHO cells were transfected with a vector expressingendosialin or mock cDNA. Cells were confirmed to express cell surfaceendosialin (CHOTEM1) while those transfected with mock (CHOK1) did not.Cells were then tested for the ability to bind EMP Collagen Type I (COLI) alone or in combination with anti-endosialin antibody M4 or controlIgG. As shown, over-expression of endosialin results in increased cellbinding to COL I which can be blocked by endosialin inhibitors such asM4 in contrast to control molecule (IgG). RbtTEM1 also suppressedFc-TEM1 binding to COL I (data not shown).

FIG. 11 shows endosialin-mediated cellular binding to EMP collagen. CHOcells were transfected with a vector expressing endosialin or mock cDNA.Cells were confirmed to express cell surface endosialin (CHOTEM1) whilethose transfected with mock (CHOK1) did not. Cells were then tested forthe ability to bind EMP collagen type I. As shown, over-expression ofendosialin results in increased cell binding to COL I.

FIG. 12 shows mediation of cell migration by endosialin and inhibitionthereof by anti-endosialin antibody M4. The ability of M4 to inhibit themigration of CHO-TEM1 and CHO-K1 cells through MATRIGEL- (FIG. 12A) orFN- (FIG. 12B) coated membranes was determined. Cells were added to thetop chamber and allowed to migrate for 48 hours at 37° C. The membranewas removed and the number of migrated cells was determined using theCELLTITER-GLO Luminescence Cell Viability Assay. Where indicated, cellswere treated with M4 or IgG isotype control for the duration ofexperiment. As shown in FIG. 12A, CHO-K1 cells exhibited modest cellmigration, whereas CHO-TEM1 cells showed >10-fold enhanced migration. M4antibody treatment, but not control IgG, abolished CHO-TEM1 cellmigration. Similar results were observed in migration experiments usingtranswell chambers coated with FN (FIG. 12B).

FIG. 13 shows endosialin enhancement of cellular pathways. CHO cellswere transfected with a vector expressing endosialin or mock cDNA. Cellswere confirmed to express cell surface endosialin (CHOTEM1) while thosetransfected with mock (CHOK1) did not. Cells were then tested for theability to upregulate cellular pathways. One such pathway is the MMP9pathway, which plays a role in cellular migration. As shown,over-expression of endosialin results in increased MMP-9 activity incontrast to control cells.

FIG. 14 shows the effect of blocking endosialin on β integrinactivation. Human embryonic kidney 293 (HEK293) cells were transfectedwith a vector expressing endosialin or mock cDNA. Cells were confirmedto express cell surface endosialin (293TEM1) while those transfectedwith mock (293T) did not. Cells were then tested for the ability toupregulate cellular pathways. One such pathway is the integrin pathwaywhich plays a role in cellular migration. As shown, over-expression ofendosialin results in increased integrin β1 activity (FIG. 14B) incontrast to control cells while direct effect on cell surface β1expression is not changed (FIG. 14A). Treatment of cells with theendosialin inhibitor M4 resulted in suppressed integrin activity whileno effect on cell surface levels were observed (FIG. 14B). These datashow the ability to use endosialin inhibitors to suppress integrinfunction in endosialin-expressing cells.

FIG. 15 illustrates that antibody M4.1 recognizes unreduced human TEM-1in CHO-TEM-1 cells and human primary pericytes but not murine TEM-1 inmouse 2H11 cells. Rabbit polyclonal against human TEM-1 (rabPAb TEM-1)recognizes human TEM-1 in CHO-TEM-1 cells and human pericytes, but alsomurine TEM-1 in mouse 2H11 cells. Neither M4.1 nor rabPAb TEM-1 reactedagainst lysates from parental CHO-K1 cells or mouse NS0 and MS1 cellsdue to lack of TEM-1 expression in these cells. Only rabPAb TEM-1reacted with reduced human TEM-1, albeit to a lesser extent whencompared to unreduced TEM-1.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Various terms relating to the methods and other aspects of the presentinvention are used throughout the specification and claims. Such termsare to be given their ordinary meaning in the art unless otherwiseindicated. Other specifically defined terms are to be construed in amanner consistent with the definition provided herein.

It is to be understood that this invention is not limited to particularmethods, reagents, compounds, compositions or biological systems, whichcan, of course, vary. It is also to be understood that the terminologyused herein is for the purpose of describing particular embodimentsonly, and is not intended to be limiting.

As used in this specification and the appended claims, the singularforms “a”, “an” and “the” include plural referents unless the contentclearly dictates otherwise. Thus, for example, reference to “a cell”includes a combination of two or more cells, and the like.

Each range recited herein includes all combinations and sub-combinationsof ranges, as well as specific numerals contained therein.

The term “about” as used herein when referring to a measurable valuesuch as an amount, a temporal duration, and the like, is meant toencompass variations of ±20% or ±10%, more preferably ±5%, even morepreferably ±1%, and still more preferably ±0.1% from the specifiedvalue, as such variations are appropriate to perform the disclosedmethods.

“Endosialin specific assay” (ESA) refers to assays that can be used toidentify compounds that can directly or indirectly perturb endosialinexpression or biological activity that results in modified direct orindirect binding of endosialin-expressing cells or endosialin to EMPsvia endosialin or integrin-mediated mechanisms as well as modifycellular endogenous pathways such as but not limited to matrixmetalloprotease (MMPs) and/or cellular proliferation or survival.

“Polynucleotide,” synonymously referred to as “nucleic acid” or “nucleicacid molecule,” refers to any polyribonucleotide orpolydeoxyribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA. “Polynucleotides” include, without limitation single- anddouble-stranded DNA, DNA that is a mixture of single- anddouble-stranded regions, single- and double-stranded RNA, and RNA thatis mixture of single- and double-stranded regions, hybrid moleculescomprising DNA and RNA that may be single-stranded or, more typically,double-stranded or a mixture of single- and double-stranded regions. Inaddition, “polynucleotide” refers to triple-stranded regions comprisingRNA or DNA or both RNA and DNA. The term polynucleotide also includesDNAs or RNAs containing one or more modified bases and DNAs or RNAs withbackbones modified for stability or for other reasons. “Modified” basesinclude, for example, tritylated bases and unusual bases such asinosine. A variety of modifications can be made to DNA and RNA; thus,“polynucleotide” embraces chemically, enzymatically or metabolicallymodified forms of polynucleotides as typically found in nature, as wellas the chemical forms of DNA and RNA characteristic of viruses andcells. “Polynucleotide” also embraces relatively short nucleic acidchains, often referred to as oligonucleotides.

A “vector” is a replicon, such as plasmid, phage, cosmid, or virus towhich another nucleic acid segment may be operably inserted so as tobring about the replication or expression of the segment.

“Polypeptide,” “peptide” and “protein” are used interchangeably hereinto refer to a polymer of amino acid residues. The terms apply to aminoacid polymers in which one or more amino acid residue is an artificialchemical mimetic of a corresponding naturally occurring amino acid, aswell as to naturally occurring amino acid polymers and non-naturallyoccurring amino acid polymers. Polypeptides of the invention includeconservatively modified variants. One of skill will recognize thatsubstitutions, deletions or additions to a nucleic acid, peptide,polypeptide, or protein sequence which alter, add or delete a singleamino acid or a small percentage of amino acids in the encoded sequenceis a “conservatively modified variant” where the alteration results inthe substitution of an amino acid with a chemically similar amino acid.Conservative substitution tables providing functionally similar aminoacids are well known in the art. Such conservatively modified variantsare in addition to and do not exclude polymorphic variants, interspecieshomologs, and alleles of the invention.

The term “express,” “expressed,” or “expression” of a nucleic acidmolecule refers to the biosynthesis of a gene product. The termencompasses the transcription of a gene into RNA. For example, but notby way of limitation, a regulatory gene such as an antisense nucleicacid or interfering nucleic acid can be expressed by transcription asantisense RNA or RNAi or shRNA. The term also encompasses translation ofRNA into one or more polypeptides, and encompasses all naturallyoccurring post-transcriptional and post-translational modifications.

A cell has been “transformed” or “transfected” by exogenous orheterologous nucleic acids such as DNA when such DNA has been introducedinside the cell. The transforming DNA may or may not be integrated(covalently linked) into the genome of the cell. In prokaryotes, yeast,and mammalian cells for example, the transforming DNA may be maintainedon an episomal element such as a plasmid. With respect to eukaryoticcells, a stably transformed cell, or “stable cell” is one in which thetransforming DNA has become integrated into a chromosome so that it isinherited by daughter cells through chromosome replication. Thisstability is demonstrated by the ability of the eukaryotic cell toestablish cell lines or clones comprised of a population of daughtercells containing the transforming DNA. A “clone” is a population ofcells derived from a single cell or common ancestor by mitosis. A “cellline” is a clone of a primary cell that is capable of stable growth invitro for many generations.

As used herein, “test compound” refers to any purified molecule,substantially purified molecule, molecules that are one or morecomponents of a mixture of compounds, or a mixture of a compound withany other material that can be utilized in the methods of the presentinvention. Test compounds can be organic or inorganic chemicals, orbiomolecules, and all fragments, analogs, homologs, conjugates, andderivatives thereof. “Biomolecules” include proteins, polypeptides,nucleic acids, lipids, monosaccharides, polysaccharides, and allfragments, analogs, homologs, conjugates, and derivatives thereof. Testcompounds can be of natural or synthetic origin, and can be isolated orpurified from their naturally occurring sources, or can be synthesizedde novo. Test compounds can be defined in terms of structure orcomposition, or can be undefined. The compound can be an isolatedproduct of unknown structure, a mixture of several known products, or anundefined composition comprising one or more compounds. Examples ofundefined compositions include cell and tissue extracts, growth mediumin which prokaryotic, eukaryotic, and archaebacterial cells have beencultured, fermentation broths, protein expression libraries, and thelike.

“Knockdown” refers to a cell or organism having reduced expression ofone or more genes. As will be appreciated by those skilled in the art, aknockdown will exhibit at least about a 50% reduction in expression,preferably will exhibit at least about a 67% reduction in expression,and more preferably will exhibit at least about a 75% reduction inexpression, although higher reductions are possible, including at leastabout a 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or more reduction in expression.

“Inhibit” or “inhibition” or “interfere” means to reduce, decrease,block, prevent, delay, suppress, inactivate, desensitize, stop, ordownregulate the biological activity or expression of a gene, geneproduct (e.g., polypeptide), or pathway of interest. In some preferredembodiments of the invention, the inhibition of the expression orbiological activity of a protein or pathway of interest, for example,endosialin or cell migration pathway, refers to a decrease (inhibitionor downregulation) of greater than from about 50% to about 99%, and morespecifically, about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69% 70%, 71%, 72%, 73%,74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more. Theinhibition may be direct, i.e., operate on the molecule or pathway ofinterest itself, or indirect, i.e., operate on a molecule or pathwaythat affects the molecule or pathway of interest.

“Recombinant” when used with reference, e.g., to a cell, or nucleicacid, protein, or vector, indicates that the cell, nucleic acid, proteinor vector, has been modified by the introduction of a heterologousnucleic acid or protein or the alteration of a native nucleic acid orprotein, or that the cell is derived from a cell so modified. Thus, forexample, recombinant cells express genes that are not found within thenative (non-recombinant) form of the cell or express native genes thatare otherwise abnormally expressed, under expressed or not expressed atall.

“Effective amount” and “therapeutically effective amount” are usedinterchangeably herein, and refer to an amount of an antibody,antigen-binding fragment, or composition, as described herein, effectiveto achieve a particular biological result such as, but not limited to,biological results disclosed, described, or exemplified herein. Suchresults may include, but are not limited to, the treatment of diseaseassociated with angiogenesis or neovascularization, as determined by anymeans suitable in the art.

As used herein, “measure” or “determine” refers to any qualitative orquantitative determinations.

“Endosialin ligand” refers to any chemical, biomolecule, complex, oranalog, homolog, or derivative thereof that can bind to, interact with,stimulate, and/or alter expression of endosialin.

Except when noted, “subject” or “patient” are used interchangeably andrefer to mammals such as human patients and non-human primates, as wellas experimental animals such as rabbits, dogs, cats, rats, mice, andother animals. Accordingly, “subject” or “patient” as used herein meansany mammalian patient or subject to which the compositions of theinvention can be administered.

“Angiogenesis” refers to the formation of new blood vessels.

“Neovascularization” refers to a pathological proliferation of new bloodvessels in a tissue(s) or organ(s) that normally do(es) not containblood vessels, or a pathological proliferation of blood vessels of adifferent type or quantity than normal for a particular tissue or organ.

“Epitope” refers to an immunological determinant of an antigen thatserves as an antibody-binding site. As used herein, the term“conformational epitope” refers to a discontinuous epitope formed by aspatial relationship between amino acids of an antigen other than anunbroken series of amino acids.

“Isolated” means altered “by the hand of man” from the natural state. Ifa molecule or composition occurs in nature, it has been “isolated” if ithas been changed or removed from its original environment, or both. Forexample, a polynucleotide or a polypeptide naturally present in a livingplant or animal is not “isolated,” but the same polynucleotide orpolypeptide separated from the coexisting materials of its natural stateis “isolated” as the term is employed herein.

“Substantially the same” with respect to nucleic acid or amino acidsequences, means at least about 65% identity between two or moresequences. Preferably, the term refers to at least about 70% identitybetween two or more sequences, more preferably at least about 75%identity, more preferably at least about 80% identity, more preferablyat least about 85% identity, more preferably at least about 90%identity, more preferably at least about 91% identity, more preferablyat least about 92% identity, more preferably at least about 93%identity, more preferably at least about 94% identity, more preferablyat least about 95% identity, more preferably at least about 96%identity, more preferably at least about 97% identity, more preferablyat least about 98% identity, and more preferably at least about 99% orgreater identity.

It has been discovered in accordance with the present invention thatendosialin specifically interacts with extracellular matrix proteins,including fibronectin or collagen. It has also been discovered that thisinteraction promotes cell migration and further promotes and facilitatesangiogenesis. Further to these observations, it has been discovered thatdisruption of the interaction between endosialin and extracellularmatrix proteins can suppress cell migration and can suppressangiogenesis. Accordingly, the invention features methods for inhibitingthe interaction of endosialin with endosialin ligands.

In one aspect, the invention features methods for inhibiting theinteraction of endosialin expressed by an endosialin-expressing cellwith an endosialin ligand. In some preferred embodiments, the methodscomprise inhibiting endosialin expression by the cell. Inhibiting theexpression of endosialin can occur at the gene level or the proteinlevel. For example, inhibiting the expression of endosialin can comprisetargeting the DNA encoding endosialin, or targeting the mRNA transcriptof the endosialin gene.

Methods of gene regulation are known and readily practiced in the art,and are all suitable for use in the inventive methods. For example, incells specifically engineered to express a transgene encoding endosialin(e.g., SEQ ID NO:1, 3, or 5), the transgene can be placed under controlof an inducible promoter. Inducible promoters suitable for use in thisinvention will be known to those of skill in the art.

In some preferred embodiments, genes encoding endosialin can beinhibited through the use of a variety of other post-transcriptionalgene silencing (RNA silencing) techniques. RNA silencing involves theprocessing of double-stranded RNA (dsRNA) into small 21-28 nucleotidefragments by an RNase H-based enzyme (“Dicer” or “Dicer-like”). Thecleavage products, which are siRNA (small interfering RNA) or miRNA(micro-RNA) are incorporated into protein effector complexes thatregulate gene expression in a sequence-specific manner.

RNA interference (RNAi) is a mechanism of post-transcriptional genesilencing mediated by double-stranded RNA (dsRNA), which is distinctfrom antisense and ribozyme-based approaches (see Jain, Pharmacogenomics(2004) 5:239-42, for a review of RNAi and siRNA). RNA interference isuseful in a method for inhibiting the expression of endosialin in a cellor in an animal such as a human by transforming the cell, or byadministering to the animal a nucleic acid (e.g., dsRNA) that hybridizesunder stringent conditions to a gene encoding endosialin, and attenuatesexpression of the target gene. RNA interference provides shRNA or siRNAthat comprise multiple sequences that target one or more regions of theendosialin gene. Double stranded RNA (dsRNA) molecules (shRNA or siRNA)are believed to direct sequence-specific degradation of mRNA in cells ofvarious types after first undergoing processing by an RNase III-likeenzyme called DICER (Bernstein E et al. (2001) Nature 409:363-366) intosmaller dsRNA molecules comprised of two 21 nt strands, each of whichhas a 5′ phosphate group and a 3′ hydroxyl, and includes a 19 nt regionprecisely complementary with the other strand, so that there is a 19 ntduplex region flanked by 2 nt-3′ overhangs. RNAi is thus mediated byshort interfering RNAs (siRNA), which typically comprise adouble-stranded region approximately 19 nucleotides in length with 1-2nucleotide 3′ overhangs on each strand, resulting in a total length ofbetween approximately 21 and 23 nucleotides. In mammalian cells, dsRNAlonger than approximately 30 nucleotides typically induces nonspecificmRNA degradation via the interferon response. However, the presence ofsiRNA in mammalian cells, rather than inducing the interferon response,results in sequence-specific gene silencing.

Viral vectors or DNA vectors encode short hairpin RNA (shRNA), which areprocessed in the cell cytoplasm to short interfering RNA (siRNA). Ingeneral, a short, interfering RNA (siRNA) comprises an RNA duplex thatis preferably approximately 19 basepairs long and optionally furthercomprises one or two single-stranded overhangs or loops. An siRNA maycomprise two RNA strands hybridized together, or may alternativelycomprise a single RNA strand that includes a self-hybridizing portion.siRNAs may include one or more free strand ends, which may includephosphate and/or hydroxyl groups. siRNAs typically include a portionthat hybridizes under stringent conditions with a target transcript. Onestrand of the siRNA (or, the self-hybridizing portion of the siRNA) istypically precisely complementary with a region of the targettranscript, meaning that the siRNA hybridizes to the target transcriptwithout a single mismatch. In certain embodiments of the invention inwhich perfect complementarity is not achieved, it is generally preferredthat any mismatches be located at or near the siRNA termini.

siRNAs have been shown to downregulate gene expression when transferredinto mammalian cells by such methods as transfection, electroporation,cationic liposome-mediated transfection, or microinjection, or whenexpressed in cells via any of a variety of plasmid-based approaches. RNAinterference using siRNA is reviewed in, e.g., Tuschl (2002) Nat.Biotechnol. 20:446-8; Yu J-Y et al. (2002) Proc. Natl. Acad. Sci. USA,99:6047-52; Sui G et al. (2002) Proc. Natl. Acad. Sci. USA, 99:5515-20;Paddison et al. (2002) Genes and Dev., 16:948-58; Brummelkamp et al.(2002) Science, 296:550-3, 2002; Miyagashi et al. (2002) Nat.Biotechnol., 20:497-500; and, Paul et al. (2002) Nat. Biotechnol.,20:505-8. As described in these and other references, the siRNA mayconsist of two individual nucleic acid strands or of a single strandwith a self-complementary region capable of forming a hairpin(stem-loop) structure. A number of variations in structure, length,number of mismatches, size of loop, identity of nucleotides inoverhangs, etc., are consistent with effective siRNA-triggered genesilencing. While not wishing to be bound by any theory, it is thoughtthat intracellular processing (e.g., by DICER) of a variety of differentprecursors results in production of siRNA capable of effectivelymediating gene silencing. Generally it is preferred to target exonsrather than introns, and it may also be preferable to select sequencescomplementary to regions within the 3′ portion of the target transcript.Generally it is preferred to select sequences that contain approximatelyequimolar ratio of the different nucleotides and to avoid stretches inwhich a single residue is repeated multiple times.

siRNAs may thus comprise RNA molecules having a double-stranded regionapproximately 19 nucleotides in length with 1-2 nucleotide 3′ overhangson each strand, resulting in a total length of between approximately 21and 23 nucleotides. As used herein, siRNAs also include various RNAstructures that may be processed in vivo to generate such molecules.Such structures include RNA strands containing two complementaryelements that hybridize to one another to form a stem, a loop, andoptionally an overhang, preferably a 3′ overhang. Preferably, the stemis approximately 19 bp long, the loop is about 1-20, more preferablyabout 4-10, and most preferably about 6-8 nt long and/or the overhang isabout 1-20, and more preferably about 2-15 nt long. In certainembodiments of the invention the stem is minimally 19 nucleotides inlength and may be up to approximately 29 nucleotides in length. Loops of4 nucleotides or greater are less likely subject to steric constraintsthan are shorter loops and therefore may be preferred. The overhang mayinclude a 5′ phosphate and a 3′ hydroxyl. The overhang may, but need notcomprise a plurality of U residues, e.g., between 1 and 5 U residues.Classical siRNAs as described above trigger degradation of mRNAs towhich they are targeted, thereby also reducing the rate of proteinsynthesis. In addition to siRNAs that act via the classical pathway,certain siRNAs that bind to the 3′ UTR of a template transcript mayinhibit expression of a protein encoded by the template transcript by amechanism related to but distinct from classic RNA interference, e.g.,by reducing translation of the transcript rather than decreasing itsstability. Such RNAs are referred to as microRNAs (miRNAs) and aretypically between approximately 20 and 26 nucleotides in length, e.g.,22 nt in length. It is believed that they are derived from largerprecursors known as small temporal RNAs (stRNAs) or mRNA precursors,which are typically approximately 70 nt long with an approximately 4-15nt loop (Grishok et al. (2001) Cell, 106:23-4; Hutvagner et al. (2001)Science, 293:834-8; Ketting et al. (2001) Genes Dev., 15:2654-9).Endogenous RNAs of this type have been identified in a number oforganisms including mammals, suggesting that this mechanism ofpost-transcriptional gene silencing may be widespread (Lagos-Quintana etal. (2001) Science, 294:853-8, 2001; Pasquinelli (2002) Trends Gen.,18:171-3). MicroRNAs have been shown to block translation of targettranscripts containing target sites in mammalian cells (Zeng et al.(2002) Mol. Cell, 9:1327-33).

siRNAs such as naturally occurring or artificial (i.e., designed byhumans) mRNAs that bind within the 3′ UTR (or elsewhere in a targettranscript) and inhibit translation may tolerate a larger number ofmismatches in the siRNA/template duplex, and particularly may toleratemismatches within the central region of the duplex. In fact, there isevidence that some mismatches may be desirable or required as naturallyoccurring stRNAs frequently exhibit such mismatches as do mRNAs thathave been shown to inhibit translation in vitro. For example, whenhybridized with the target transcript such siRNAs frequently include twostretches of perfect complementarity separated by a region of mismatch.A variety of structures are possible. For example, the mRNA may includemultiple areas of nonidentity (mismatch). The areas of nonidentity(mismatch) need not be symmetrical in the sense that both the target andthe mRNA include nonpaired nucleotides. Typically the stretches ofperfect complementarity are at least 5 nucleotides in length, e.g., 6,7, or more nucleotides in length, while the regions of mismatch may be,for example, 1, 2, 3, or 4 nucleotides in length.

Hairpin structures designed to mimic siRNAs and mRNA precursors areprocessed intracellularly into molecules capable of reducing orinhibiting expression of target transcripts (McManus et al. (2002) RNA8:842-50). These hairpin structures, which are based on classical siRNAsconsisting of two RNA strands forming a 19 bp duplex structure areclassified as class I or class II hairpins. Class I hairpins incorporatea loop at the 5′ or 3′ end of the antisense siRNA strand (i.e., thestrand complementary to the target transcript whose inhibition isdesired) but are otherwise identical to classical siRNAs. Class IIhairpins resemble mRNA precursors in that they include a 19 nt duplexregion and a loop at either the 3′ or 5′ end of the antisense strand ofthe duplex in addition to one or more nucleotide mismatches in the stem.These molecules are processed intracellularly into small RNA duplexstructures capable of mediating silencing. They appear to exert theireffects through degradation of the target mRNA rather than throughtranslational repression as is thought to be the case for naturallyoccurring mRNAs and siRNAs.

Thus, it is evident that a diverse set of RNA molecules containingduplex structures is able to mediate silencing through variousmechanisms. For the purposes of the present invention, any such RNA, oneportion of which binds to a target transcript and reduces itsexpression, whether by triggering degradation, by inhibitingtranslation, or by other means, is considered to be an siRNA, and anystructure that generates such an siRNA (i.e., serves as a precursor tothe RNA) is useful in the practice of the present invention.

A further method of RNA interference for use in the present invention isthe use of short hairpin RNAs (shRNA). A plasmid containing a DNAsequence encoding for a particular desired siRNA sequence is deliveredinto a target cell via transfection or virally-mediated infection. Oncein the cell, the DNA sequence is continuously transcribed into RNAmolecules that loop back on themselves and form hairpin structuresthrough intramolecular base pairing. These hairpin structures, onceprocessed by the cell, are equivalent to transfected siRNA molecules andare used by the cell to mediate RNAi of the desired protein. The use ofshRNA has an advantage over siRNA transfection as the former can lead tostable, long-term inhibition of protein expression Inhibition of proteinexpression by transfected siRNAs is a transient phenomenon that does notoccur for times periods longer than several days. In some cases, thismay be preferable and desired. In cases where longer periods of proteininhibition are necessary, shRNA mediated inhibition is preferable. Theuse of shRNA is particularly preferred. Typically, siRNA-encodingvectors are constructs comprising a promoter, a sequence of the targetgene to be silenced in the “sense” orientation, a spacer, the antisenseof the target gene sequence, and a terminator.

Inhibition of the expression of endosialin can also be effectuated byother means that are known and readily practiced in the art. Forexample, antisense nucleic acids can be used. Antisense RNA transcriptshave a base sequence complementary to part or all of any other RNAtranscript in the same cell. Such transcripts have been shown tomodulate gene expression through a variety of mechanisms including themodulation of RNA splicing, the modulation of RNA transport and themodulation of the translation of mRNA (Denhardt (1992) Ann. N Y Acad.Sci., 660:70-6, 1992; Nellen et al. (1993) Trends Biochem. Sci.,18:419-23; and, Baker et al. (1999) Biochim. Biophys. Acta., 1489:3-18). Accordingly, in certain embodiments of the invention, inhibitionof endosialin in a cell is accomplished by expressing an antisensenucleic acid molecule in the cell.

Antisense nucleic acids are generally single-stranded nucleic acids(DNA, RNA, modified DNA, or modified RNA) complementary to a portion ofa target nucleic acid (e.g., an mRNA transcript) and therefore able tobind to the target to form a duplex. Typically, they areoligonucleotides that range from 15 to 35 nucleotides in length but mayrange from 10 up to approximately 50 nucleotides in length. Bindingtypically reduces or inhibits the function of the target nucleic acid,such as a gene encoding endosialin. For example, antisenseoligonucleotides may block transcription when bound to genomic DNA,inhibit translation when bound to mRNA, and/or lead to degradation ofthe nucleic acid. Inhibition of the expression of endosialin can beachieved by the administration of antisense nucleic acids or peptidenucleic acids comprising sequences complementary to those of the mRNAthat encodes the endosialin protein. Antisense technology and itsapplications are well known in the art and are described in Phillips(ed.) Antisense Technology, Methods Enzymol., 2000, Volumes 313 and 314,Academic Press, San Diego, and references mentioned therein. See alsoCrooke (ed.) “ANTISENSE DRUG TECHNOLOGY: PRINCIPLES, STRATEGIES, ANDAPPLICATIONS” (1^(st) Edition) Marcel Dekker and references citedtherein.

Antisense oligonucleotides can be synthesized with a base sequence thatis complementary to a portion of any RNA transcript in the cell.Antisense oligonucleotides can modulate gene expression through avariety of mechanisms including the modulation of RNA splicing, themodulation of RNA transport and the modulation of the translation ofmRNA. Various properties of antisense oligonucleotides includingstability, toxicity, tissue distribution, and cellular uptake andbinding affinity may be altered through chemical modifications including(i) replacement of the phosphodiester backbone (e.g., peptide nucleicacid, phosphorothioate oligonucleotides, and phosphoramidateoligonucleotides), (ii) modification of the sugar base (e.g.,2′-O-propylribose and 2′-methoxyethoxyribose), and (iii) modification ofthe nucleoside (e.g., C-5 propynyl U, C-5 thiazole U, and phenoxazine C)(Wagner (1995) Nat. Medicine, 1:1116-8; Varga et al. (1999) Immun.Lett., 69:217-24; Neilsen (1999) Curr. Opin. Biotech., 10:71-5; andWoolf (1990) Nucleic Acids Res., 18:1763-9).

Inhibition of endosialin gene expression can also be effectuated by useof ribozymes. Certain nucleic acid molecules referred to as ribozymes ordeoxyribozymes have been shown to catalyze the sequence-specificcleavage of RNA molecules. The cleavage site is determined bycomplementary pairing of nucleotides in the RNA or DNA enzyme withnucleotides in the target RNA. Thus, RNA and DNA enzymes can be designedto cleave to any RNA molecule, thereby increasing its rate ofdegradation (Cotten et al. (1989) EMBO J., 8:861-6; and, Usman et al.(1996) Curr. Opin. Struct. Biol., 1:527-33). Hammerhead ribozymes arealso routinely used in gene regulation (Lyngstadaas (2001) Crit. Rev.Oral Biol. Med., 12:469-78).

In preferred aspects of the invention, the cells targeted by theinventive methods can be specifically transformed withtranscription-silencing nucleic acids such as shRNA or siRNA, or can betransformed with vectors encoding such nucleic acids such that the cellexpresses the inhibitory nucleic acid molecules. Transformation of thecells can be carried out according to any means suitable in the art,including those described and exemplified herein.

Decoy oligonucleotides are also suitable for regulating the expressionof endosialin-encoding genes. Recent clinical trials have tested theability of decoy oligonucleotides to sequester pathogenic proteins.Decoy oligonucleotides generally contain an enhancer element that canpenetrate cells, and once inside cells, the decoy oligonucleotides bindto sequence-specific DNA-binding proteins and interfere withtranscription (Fichou et al., (2006) Trends Biotechnol., 24:563-70;Nakamura et al. (2002) In Vivo, 16:45-8; Tomita et al. (1997) Exp.Nephrol., 5:429-34).

Genetic regulation of endosialin expression can also be effectuated byknockdown of the gene encoding endosialin. As will be appreciated bythose of skill in the art, the sequence of the endosialin gene (from anyorganism of interest), for example, SEQ ID NO: 1, 3, or 5, can be usedto generate nucleic acid molecules and vectors for knockdown expressionof the endosialin gene. Considered in terms of their sequences, thenucleic acid molecules that encode regulatory, particularly inhibitory,sequences derived from SEQ ID NOs: 1, 3, and 5, include allelicvariants, homologs, and natural mutants of SEQ ID NOs: 1, 3, and 5.Because such variants and homologs are expected to possess certaindifferences in nucleotide sequence, this invention provides isolatedpolynucleotides that have at least about 60%, preferably at least about61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69% or 70%, more preferably atleast about 71%, 72%, 73%, 74%, 75%, 76%, 77%. 78%, 79%, or 80%, evenmore preferably 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and evenmore preferably 90%, 91%, 92%, 93%, 94%, 95%, and most preferably 96%,97%, 98% and 99% or more identity with any knockdown nucleic acidderived from SEQ ID NOs: 1, 3, or 5. Because of the natural sequencevariation likely to exist among genes encoding these regulatorysequences in different organisms, one skilled in the art would expect tofind this level of variation, while still maintaining the uniqueproperties of the knockdown polynucleotides. Accordingly, such variantsand homologs are considered substantially the same as one another andare included within the scope of the present invention.

Knockdown nucleic acid molecules can be prepared by two general methods:(1) they may be synthesized from appropriate nucleotide triphosphates,or (2) they may be isolated from biological sources. Both methodsutilize protocols well known in the art.

The availability of nucleotide sequence information such as the entirenucleic acid sequence of endosialin, for example, SEQ ID NOs:1, 3, and5, enables preparation of an isolated nucleic acid molecule of theinvention by oligonucleotide synthesis. Synthetic oligonucleotides maybe prepared by the phosphoramadite method employed in the AppliedBiosystems 38A DNA Synthesizer or similar devices. The resultantconstruct may be purified according to methods known in the art, such ashigh performance liquid chromatography (HPLC). A synthetic DNA moleculeso constructed may then be cloned and amplified in an appropriatevector.

Knockdown nucleic acids may be maintained as DNA in any convenientcloning vector. In some preferred aspects, clones are maintained inplasmid cloning/expression vector, either of which can be propagated ina suitable prokaryotic or eukaryotic host cell.

Knockdown nucleic acid molecules include cDNA, genomic DNA, RNA, andfragments thereof which may be single-, double-, or eventriple-stranded. Thus, this invention provides oligonucleotides (senseor antisense strands of DNA or RNA) having sequences capable ofhybridizing with at least one sequence of a nucleic acid molecule of thepresent invention, in particular, SEQ ID NOs: 1, 3, or 5. Sucholigonucleotides are useful as probes for detecting genes encodingendosialin, or for the positive or negative regulation of expression ofgenes encoding endosialin at or before translation of the mRNA into theprotein. Methods in which oligonucleotides or polynucleotides may beutilized as probes for such assays include, but are not limited to: (1)in situ hybridization; (2) Southern hybridization (3) northernhybridization; and (4) assorted amplification reactions such aspolymerase chain reactions (PCR) and ligase chain reaction (LCR).

Also featured in accordance with the present invention are vectors andkits for producing transgenic host cells that comprise a polynucleotideencoding a regulatory sequence for inhibiting the expression ofendosialin, or homolog, analog or variant thereof in a sense orantisense orientation, or a construct under control of cell ortissue-specific promoters and/or other regulatory sequences. Suchvectors are suitable for modulating, and preferably inhibiting, theexpression of endosialin.

Suitable host cells include, but are not limited to, plant cells,bacterial cells, yeast and other fungal cells, insect cells andmammalian cells that express endosialin. The cells can be neoplasticallytransformed. More preferred are human cells.

Vectors for transforming a wide variety of these host cells are wellknown to those of skill in the art. They include, but are not limitedto, plasmids, phagemids, cosmids, baculoviruses, bacmids, bacterialartificial chromosomes (BACs), yeast artificial chromosomes (YACs), aswell as other bacterial, yeast and viral vectors.

The coding region of a regulatory sequence can be placed under apowerful constitutive promoter, such as the promoters for the followinggenes: hypoxanthine phosphoribosyl transferase (HPRT), adenosinedeaminase, pyruvate kinase, beta-actin, human myosin, human hemoglobin,human muscle creatine, and others. In addition, many viral promotersfunction constitutively in eukaryotic cells and are suitable for use inthe present invention. Such viral promoters include without limitation,Cytomegalovirus (CMV) immediate early promoter, the early and latepromoters of SV40, the Mouse Mammary Tumor Virus (MMTV) promoter, thelong terminal repeats (LTRs) of Maloney leukemia virus, HumanImmunodeficiency Virus (HIV), Epstein Barr Virus (EBV), Rous SarcomaVirus (RSV), and other retroviruses, and the thymidine kinase promoterof Herpes Simplex Virus. Other promoters are known to those of ordinaryskill in the art. In one embodiment, the coding region of the regulatorysequence is placed under an inducible promoter such as themetallothionein promoter, tetracycline-inducible promoter,doxycycline-inducible promoter, promoters that contain one or moreinterferon-stimulated response elements (ISRE) such as protein kinase R2′,5′-oligoadenylate synthetases, Mx genes, ADAR1, and the like. Othersuitable inducible promoters will be known to those of skill in the art.

Knockdown vectors can be used to transform various endosialin-expressingcells with regulatory nucleic acid sequences. Numerous techniques areknown in the art for the introduction of foreign genes into cells andmay be used to construct recombinant cells for purposes of carrying outthe inventive methods, in accordance with the various embodiments of theinvention. The technique used should provide for the stable transfer ofthe heterologous gene sequence to the host cell, such that theheterologous gene sequence is heritable and expressible by the cellprogeny, and so that the necessary development and physiologicalfunctions of the recipient cells are not disrupted. Techniques which maybe used include but are not limited to chromosome transfer (e.g., cellfusion, chromosome-mediated gene transfer, micro cell-mediated genetransfer), physical methods (e.g., transfection, spheroplast fusion,microinjection, electroporation, liposome carrier), viral vectortransfer (e.g., recombinant DNA viruses, recombinant RNA viruses) andthe like (described in Cline (1985) Pharmac. Ther., 29:69-92).

Knockdown cells with inhibited expression of endosialin can be createdby inhibiting the translation of mRNA encoding the transport protein by“post-transcriptional gene silencing.” The gene from the speciestargeted for down-regulation, or a fragment thereof, may be utilized tocontrol the production of the encoded protein. Full-length antisensemolecules can be used for this purpose. Alternatively, antisenseoligonucleotides targeted to specific regions of the mRNA that arecritical for translation may be utilized. Antisense molecules may beprovided in situ by transforming cells with a DNA construct which, upontranscription, produces the antisense RNA sequences. Such constructs canbe designed to produce full-length or partial antisense sequences. Thisgene silencing effect can be enhanced by transgenically over-producingboth sense and antisense RNA of the gene coding sequence so that a highamount of dsRNA is produced (for example, see Waterhouse et al. (1998)Proc. Natl. Acad. Sci. U.S.A., 95:13959-64). In this regard, dsRNAcontaining sequences that correspond to part or all of at least oneintron have been found particularly effective. In one embodiment, partor all of the coding sequence antisense strand is expressed by atransgene. In another embodiment, hybridizing sense and antisensestrands of part or all of the coding sequence for one endosialin aretransgenically expressed.

Cells that can be targeted by or otherwise used in the methods of theinvention include endosialin-expressing cells that naturally expressendosialin or cells transfected with a recombinant plasmid expressingendosialin. Primary endosialin-expressing cells of the invention can beisolated from tissues or purchased from vendors selling endothelialcells, such as but not limited to HMVEC or HMVEC as well as primary andcultured fibroblasts. Transfected cells of the invention include anyinsect expression cell line known, such as for example, Spodopterafrugiperda cells. The expression cell lines may also be yeast celllines, such as, for example, Saccharomyces cerevisiae andSchizosaccharomyces pombe cells. The expression cells may also bemammalian cells such as, for example Chinese Hamster Ovary, baby hamsterkidney cells, human embryonic kidney line 293, normal dog kidney celllines, normal cat kidney cell lines, monkey kidney cells, African greenmonkey kidney cells, COS cells, and non-tumorigenic mouse myoblast G8cells, fibroblast cell lines, myeloma cell lines, mouse NIH/3T3 cells,LMTK cells, mouse sertoli cells, human cervical carcinoma cells, buffalorat liver cells, human lung cells, human liver cells, mouse mammarytumor cells, TR1 cells, MRC 5 cells, and FS4 cells.

Inhibiting the expression of endosialin inhibits the interaction ofendosialin with any endosialin ligand. Endosialin ligands includeextracellular matrix proteins such as fibronectin and collagen.

Also featured in accordance with the present invention are methods forinhibiting the interaction of endosialin expressed by an endosialinexpressing cell with an endosialin ligand that comprise blocking orobstructing the endosialin expression by the cell. Thus, for example, aphysical barrier serves to inhibit, impede, or otherwise hinder theinteraction of expressed endosialin with an endosialin ligand. Anychemical or biomolecule can serve to obstruct this interaction. Forexample, small molecules, polypeptides, antibodies, and antigen-bindingfragments thereof that specifically bind to endosialin, or in thealternative, specifically bind to an endosialin ligand can be used inthis methods.

In some preferred embodiments, inhibiting the interaction of anendosialin-expressing cell with a ligand for endosialin comprisesinhibiting the binding of the endosialin ligand to the expressedendosialin. For example, the interaction between endosialin and itsligand is hindered, blocked, impeded, or otherwise obstructed with amolecular barrier. In this way, access to the cell by the ligand is thushindered, inhibited, blocked, impeded, obstructed or prevented.Obstruction of the endosialin can occur by any means suitable in theart, such as with a chemical or biomolecule.

For example, chemicals suitable for use in the inventive methodsinclude, but are not limited to, amino acid structures, steroids,cyclines, anthracenes, heavy metals, quinilone, terpenes, phenolics,glycosides, alkyloids, lipids, etc. or mixtures thereof that can exert abiological effect on endosialin-expressing cells. Chemicals can begenerated by chemical synthesis or derived from biocatalysis or derivedfrom biological fluids. Chemicals can be derived from human, non-humanmammalian, plant, yeast, fungi and/or prokaryotic sources.

In some embodiments, competitive inhibitors are employed to inhibit theinteraction of endosialin or an endosialin-expressing cell with a ligandfor endosialin. A “competitive inhibitor” competes with the ligand forthe binding site to endosialin. In some embodiments, the competitiveinhibitors are endosialin ligands, for example, collagen (e.g., collagenI or IV) or fibronectin, or endosialin-binding fragments thereof. Mostpreferred competitive inhibitors are the 70 kDa N-terminal fragment offibronectin, the 45 kDa gelatin binding fragment of fibronectin, and the30 kDa heparin binding fragment of fibronectin.

In highly preferred embodiments, antibodies or antigen-binding fragmentsthereof are used to obstruct the interaction of expressed endosialinwith endosialin ligands. The antibodies or antigen-binding fragments canbe specific for an epitope on endosialin, or can be specific for anepitope on an endosialin ligand. Antibodies and antigen-bindingfragments thereof specific for endosialin are more preferred. Antibodiesto ligands such as fibronectin, collagen, and the like are commerciallyavailable.

Suitable antibodies can be polyclonal or monoclonal, or can bederivatives or fragments of antibodies that retain specificity forendosialin or an endosialin ligand. The antibodies can be from any ofthe five classes of antibodies, i.e., the IgA, IgD, IgE, IgG and IgMisotypes. Suitable antibodies also include the IgY isotype generallyfound in hen or turkey serum and hen or turkey egg yolk.

Antibody derivatives and antigen-binding fragments are suitable for usein the inventive methods, and such derivatives comprise portions ofintact antibodies that retain antigen-binding specificity of the parentantibody molecule. For example, derivatives can comprise at least onevariable region (either a heavy chain or light chain variable region).Examples of suitable antibody derivatives and fragments include, withoutlimitation antibodies with polyepitopic specificity, bispecificantibodies, diabodies, and single-chain molecules, as well as Fab,F(ab′)2, Fd, Fabc, and Fv molecules, single chain (Sc) antibodies,individual antibody light chains, individual antibody heavy chains,chimeric fusions between antibody chains and other molecules, heavychain monomers or dimers, light chain monomers or dimers, dimersconsisting of one heavy and one light chain, and the like. All antibodyisotypes can be used to produce antibody derivatives and fragments.Antibody derivatives and fragments can be recombinantly produced.

Antibodies suitable for use in the inventive methods can be derived fromany species. For example, the antibodies can be mouse, rat, goat, horse,swine, bovine, chicken, rabbit, donkey, human, and the like. For use inmethods of treatment, or for administration to humans, non-human derivedantibodies can be structurally altered to be less antigenic uponadministration to a human patient.

Thus, in some embodiments of the invention, the antibodies used in theinventive methods are chimeric antibodies. Chimeric antibodies andmethods to produce them are well known and established in the art. Forexample, a chimeric antibody may comprise a mouse antigen binding domainwith a human Fc or other such structural domain.

In some embodiments, the antibodies are humanized antibodies. Humanizedantibodies can be chimeric immunoglobulins, immunoglobulin chains orfragments thereof (such as Fv, Fab, Fab′, F(ab′)2 or otherantigen-binding subsequences of antibodies) that contain minimalsequence derived from non-human immunoglobulin. For the most part,humanized antibodies are human immunoglobulins (recipient antibody) inwhich residues from a complementary-determining region (CDR) of therecipient are replaced by residues from a CDR of a non-human species(donor antibody) such as mouse, rat or rabbit having the desiredspecificity, affinity, and capacity. In some instances, Fv frameworkregion (FWR) residues of the human immunoglobulin are replaced bycorresponding non-human residues. Furthermore, humanized antibodies cancomprise residues which are found neither in the recipient antibody norin the imported CDR or framework sequences. These modifications are madeto further refine and optimize antibody performance. In general, thehumanized antibody will comprise substantially all of at least one, andtypically two, variable domains, in which all or substantially all ofthe CDR regions correspond to those of a non-human immunoglobulin andall or substantially all of the FWR regions are those of a humanimmunoglobulin sequence. The humanized antibody optimally also willcomprise at least a portion of an immunoglobulin constant region (Fc),typically that of a human immunoglobulin. For further details, see Joneset al. (1986) Nature, 321:522-5; Reichmann et al. (1988) Nature,332:323-9; and Presta (1992) Curr. Op. Struct. Biol., 2:593-6.

In preferred aspects of the invention, the antibodies are fully human.This means that the antibody is solely from human origin, or otherwiseconsists of an amino acid sequence identical to a human form of theantibody.

The antibodies of the invention can be labeled or otherwise conjugatedto various chemical or biomolecule moieties, for example, fortherapeutic or diagnostic applications. The moieties can be cytotoxic,for example, bacterial toxins, viral toxins, radioisotopes, and thelike. The moieties can be detectable labels, for example, fluorescentlabels, radiolabels, biotin, and the like. Additional moieties include,but are not limited to glycosylation, acetylation, pegylation,phosphorylation, and amidation. The antibodies useful in the methods ofthe invention may themselves by derivatized by known protecting/blockinggroups, proteolytic cleavage, linkage to a cellular ligand or otherproteins, and the like.

Those of skill in the art will recognize that antibody specificity isprimarily determined by the six CDR regions, especially H chain CDR3(Kala et al. (2002) J. Biochem., 132:535-41; Morea et al. (1998) J. Mol.Biol., 275:269-94; and, Chothia et al. (1987) J. Mol. Biol.,196:901-17). Antibody framework regions, however, can play a role inantigen-antibody interactions (Panka et al. (1988) Proc. Natl. Acad.Sci. USA, 85:3080-4), particularly with respect to their role inconformation of CDR loops (Foote et al. (1992) J. Mol. Biol.,224:487-99). Thus, antibodies suitable for use in the inventive methodscan comprise any combination of H or L chain CDR or FWR regions thatconfer antibody specificity for endosialin or endosialin ligands.

In some embodiments, the invention contemplates the use of isolatedhuman antibodies and antigen-binding fragments thereof that specificallybind to endosialin. In some embodiments, suitable antibodies orantigen-binding fragments can comprise a heavy chain comprising CDR1,CDR2, and CDR3 of SEQ ID NO:28, 30, and 32, respectively, and a lightchain comprising CDR1, CDR2, and CDR3 of SEQ ID NO: 13, 15, and 17,respectively. In some embodiments, the heavy chain CDR1, CDR2, and CDR3are encoded by nucleotide sequences of SEQ ID NO:27, 29, and 31,respectively. In some embodiments, the light chain CDR1, CDR2, and CDR3are encoded by nucleotide sequences of SEQ ID NO:12, 14, and 16,respectively. In some embodiments, the antibodies or antigen-bindingfragments can comprise a heavy chain comprising a variable domain of SEQID NO: 34 and a light chain comprising a variable domain of SEQ ID NO:19. In some embodiments, the heavy chain variable domain is encoded bythe nucleotide sequence of SEQ ID NO:33. In some embodiments, the lightchain variable domain is encoded by the nucleotide sequence of SEQ IDNO:18. In some embodiments, the antibodies or antigen-binding fragmentscan comprise a heavy chain comprising the amino acid sequence of SEQ IDNO:22 or 26 and a light chain comprising the amino acid sequence of SEQID NO:11. In some embodiments, the heavy chain is encoded by thenucleotide sequence of SEQ ID NO:21 or 25 and the light chain is encodedby the nucleotide sequence of SEQ ID NO:10. In some embodiments, theantibodies or antigen-binding fragments comprise a heavy chaincomprising SEQ ID NO:20 or 24 and a light chain comprising SEQ ID NO:9.In some embodiments, the antibodies comprise a heavy chain encoded bythe nucleic acid sequence of SEQ ID NO:8 or 23. Antibodies orantigen-binding fragments can comprise a light chain encoded by thenucleic acid sequence that comprises SEQ ID NO:7.

Antibody-producing cells producing antibodies that can be used inaccordance with the invention have been placed with the Amer. Type Cult.Coll. (10801 University Blvd., Manassas, Va. 20110-2209) on Apr. 24,2006 and on Mar. 11, 2008 and have been assigned Access. Nos. PTA-7554and PTA-9017, respectively.

It is to be understood that, because of the natural sequence variationlikely to exist among heavy and light chains and the genes encodingthem, one skilled in the art would expect to find some level ofvariation within the amino acid sequences or the genes encoding them,while still maintaining the unique binding properties (e.g., specificityand affinity) of the antibodies of the present invention. Such anexpectation is due in part to the degeneracy of the genetic code, aswell as to the known evolutionary success of conservative amino acidsequence variations, which do not appreciably alter the nature of theencoded protein. Accordingly, such variants and homologs are consideredsubstantially the same as one another and are included within the scopeof the present invention.

Variants having single or multiple amino acid substitutions, deletions,additions, or replacements that retain the biological properties (e.g.,binding affinity or immune effector activity) of the antibodiesdescribed herein are contemplated for use in the invention. The skilledperson can produce variants having single or multiple amino acidsubstitutions, deletions, additions or replacements. These variants mayinclude, for example: (a) variants in which one or more amino acidresidues are substituted with conservative or nonconservative aminoacids, (b) variants in which one or more amino acids are added to ordeleted from the polypeptide, (c) variants in which one or more aminoacids include a substituent group, and (d) variants in which thepolypeptide is fused with another peptide or polypeptide such as afusion partner, a protein tag or other chemical moiety, that may conferuseful properties to the polypeptide, such as, for example, an epitopefor an antibody, a polyhistidine sequence, a biotin moiety and the like.Antibodies of the invention may include variants in which amino acidresidues from one species are substituted for the corresponding residuein another species, either at the conserved or nonconserved positions.In other embodiments, amino acid residues at nonconserved positions aresubstituted with conservative or nonconservative residues. Thetechniques for obtaining these variants, including genetic(suppressions, deletions, mutations, etc.), chemical, and enzymatictechniques, are known to the person having ordinary skill in the art.

The present invention contemplates antibodies, or antigen-bindingfragments thereof, having amino acid sequences that are substantiallythe same as the previously described amino acid sequences. For example,such antibodies or antigen-binding fragments may include those whereinthe heavy chain CDR1, CDR2, and CDR3 are at least 90% identical to SEQID NO:28, 30, and 32, respectively, and/or wherein the light chain CDR1,CDR2, and CDR3 are at least 90% identical to SEQ ID NO: 13, 15, and 17,respectively. In some embodiments, such antibodies or antigen-bindingfragments may include those wherein the heavy chain variable domain isat least 90% identical to SEQ ID NO: 34 and/or wherein the light chainvariable domain is at least 90% identical to SEQ ID NO: 19. In someembodiments, the antibodies or antigen-binding fragments may includethose wherein the heavy chain is at least 90% identical to SEQ ID NO:22or 26 and/or wherein the light chain is at least 90% identical to SEQ IDNO:11. In some embodiments, the antibodies or antigen-binding fragmentsmay include those wherein the heavy chain is at least 90% identical toSEQ ID NO:20 or 24 and/or wherein the light chain is at least 90%identical to SEQ ID NO:9. For example, antibodies M4 and M4.1 arehumanized antibodies to human endosialin. While antibodies M4 and M4.1share a light chain sequence, they differ in their heavy chain by asingle amino acid sequence shown, for example, at residue 429 of SEQ IDNO:20 relative to residue 429 of SEQ ID NO:24. The invention furthercontemplates antibodies, or antigen-binding fragments thereof, thatcompete for binding to endosialin with antibody M4 or M4.1. Theinvention further contemplates antibodies, or antigen-binding fragmentsthereof, that bind the same epitope of endosialin as antibody M4 orM4.1.

Antibodies suitable for use in the methods of the invention can havebinding affinities for the target antigen, such as endosialin or anendosialin ligand, that include a dissociation constant (K_(D)) of lessthan 1×10⁻² M. In some embodiments, the K_(D) is less than 1×10⁻³ M. Inother embodiments, the K_(D) is less than 1×10⁻⁴M. In some embodiments,the K_(D) is less than 1×10⁻⁵ M. In still other embodiments, the K_(D)is less than 1×10⁻⁶ M. In other embodiments, the K_(D) is less than1×10⁻⁷ M. In other embodiments, the K_(D) is less than 1×10⁻⁸ M. Inother embodiments, the K_(D) is less than 1×10⁻⁹ M. In otherembodiments, the K_(D) is less than 1×10⁻¹⁰ M. In still otherembodiments, the K_(D) is less than 1×10⁻¹¹ M. In some embodiments, theK_(D) is less than 1×10⁻¹² M. In other embodiments, the K_(D) is lessthan 1×10⁻¹³ M. In other embodiments, the K_(D) is less than 1×10⁻¹⁴ M.In still other embodiments, the K_(D) is less than 1×10⁻¹⁵ M.

Specificity and/or affinity of antibodies that bind to endosialin canoptionally be optimized by directed evolution of the cells producing theantibody, by using a dominant negative allele of a mismatch repair genesuch as PMS1, PMS2, PMS2-134, PMSR2, PMSR3, MLH1, MLH2, MLH3, MLH4,MLH5, MLH6, PMSL9, MSH1, and MSH2 introduced into the antibody-producingcells. Cells containing the dominant negative mutant will becomehypermutable and accumulate mutations at a higher rate thanuntransfected control cells. A pool of the mutating cells may bescreened for clones that produce higher affinity/specificity ofantibodies or binding proteins, or that produce higher titers ofantibodies or binding proteins, or that simply grow faster or betterunder certain conditions. The technique for generating hypermutablecells using dominant negative alleles of mismatch repair genes isdescribed in U.S. Pat. No. 6,146,894. Alternatively, mismatch repair maybe inhibited using the chemical inhibitors of mismatch repair describedin WO 02/054856. The technique for enhancing antibodies using thedominant negative alleles of mismatch repair genes or chemicalinhibitors of mismatch repair may be applied to mammalian, yeast, plantor prokaryotic expression cells expressing cloned immunoglobulin orprotein genes as well. Cells expressing the dominant negative alleles orsmall molecule can be “cured” in that the dominant negative allele canbe turned off, if inducible, eliminated from the cell while the smallchemical can be removed from grow culture resulting in cells that aregenetically stable once more and no longer accumulate mutations at theabnormally high rate.

Inhibiting the expression of endosialin inhibits the interaction ofendosialin with any endosialin ligand. Endosialin ligands includeextracellular matrix proteins, such as fibronectin and collagen. Anycollagen subtype can serve as a ligand to endosialin. Collagen I andCollagen IV are more preferred.

Inhibiting the interaction of endosialin with endosialin ligandsinhibits pathways and cascades that are upregulated or otherwiseactivated as a result of this interaction. For example, endosialininteraction with endosialin ligands can promote the expression and/oractivation of adhesion molecules such as integrins, which mediate cellattachment to the extracellular matrix or to other cells, and whichmediate cell signal pathways, among other things.

Integrins tend to exist as heterodimers containing two distinct chains,an α (alpha) and β (beta) subunit. There are approximately 18 α and 8 βsubunits that have been characterized. In addition, a number of integrinsubunits exist as variants via differential splicing. The variouscombinations of alpha and beta integrin subunits results in over 24unique active integrin complexes (Hynes (2002) Cell, 110:673). Integrinsubunits penetrate the plasma membrane, and in general contain shortcytoplasmic domains of about 40-70 amino acids. Outside the cell plasmamembrane, the alpha and beta chains lie in close proximity to each otheralong a length of about 23 nm. The amino-termini of each integrin chainare juxtaposed within 5 nm of each other to form a ligand-binding regionfor EMP interaction. Integrins are categorized using several criteria.Alpha chains are classified as such because a subset of the a chainshave structural elements inserted near the amino-terminus called alpha-Adomain because it has a similar structural motif as the A-domains withinthe von Willebrand factor. Integrins carrying this domain can eitherbind to collagens (integrin complexes α1β1 and α2β1), or act ascell-cell adhesion molecules with those complexes containing integrinsof the β2 family. Two main functions of integrins are attachment of thecell to extracellular matrix proteins and signal transduction mediatedfrom the EMP-integrin binding to the cell. In addition, integrins arealso involved in a wide range of other biological activities includingbinding of viruses, such as adenovirus, Echo viruses, Hanta viruses,foot and mouth disease viruses as well as binding to cells involved inimmune patrolling and cell-cell contact for cell migration. Integrinscouple EMPs (which depends on the integrin complex) to the cytoskeletonwithin the cell. Several ligands of integrins have been identified. Themore common ligands are fibronectin, vitronectin, collagen, and laminin.The interactions between integrin, an EMP and the microfilaments insidethe cell are linked via scaffolding proteins including talin, paxillinand alpha-actinin. These interactions result in regulation of kinaseslike FAK (focal adhesion kinase) and Src kinase family members tophosphorylate substrates such as p130CAS thereby recruiting signalingadaptors such as Crk for mediating cellular responses including pathwayactivation, cellular proliferation and/or survival. Any of theseintegrin-associated functions can be assembled as a screening assay tomonitor integrin activity as a function of endosialin activity forassays to identify pharmacologic agents or effective endosialintargeting molecules of this invention. Moreover, in light of theinvention disclosed here, targeting integrins with pharmacologic agentsto endosialin in endosialin-expressing cells have broad opportunities insuppressing integrin-mediated viral infection and other pathologies.

Thus, inhibiting the interaction of endosialin with an endosialin ligandinhibits the expression and/or activation of integrin molecules on theendosialin-expressing cell. In some preferred embodiments, theexpression or activation of integrin β1, β2, or β3 is suppressed by theinhibition.

Other molecules and pathways whose expression and/or activation areaffected by the inhibition of endosialin interaction with endosialinligands include matrix metalloproteinases (MMPs). MMPs arezinc-dependent proteases that play a role in, among other things,degradation of extracellular matrix proteins, cell surface receptors,and the like. MMPs play a role in cell migration, proliferation, andangiogenesis, among other things. The MMP family of enzymes have acommon zinc binding motif (HExxHxxGxxH) within their active site, and aconserved methionine following the active site. MMPs are classified bytheir homology to one another, substrate specificity and partly on theircellular localization. They are broadly grouped into 4 classes:collagenase, stromelysins, gelatinase, and the membrane type MMPs(MT-MMPs). Collagenase-type MMPs are capable of degrading triple-helicalfibrillar collagens into distinctive fragments. These collagens are themajor components of bone and cartilage, and this class of MMPs are theonly known mammalian enzymes capable of degrading them. They includeMMP-1 (Interstitial collagenase); MMP-8 (Neutrophil collagenase); MMP-13(Collagenase 3); and MMP-18. Stromelysin-type MMP enzymes display abroad ability to cleave EMPs but are unable to cleave the triple-helicalfibrillar collagens. This class includes MMP-3 (Stromelysin 1); MMP-10(Stromelysin 2); MMP-11 (Stromelysin 3); MMP-12 (Macrophagemetalloelastase); MMP-19 (RASI-1, also referred to as stromelysin-4);and MMP-20 (enamelysin); MMP-22 (C-MMP) and MMP-27. Gelatinase-type MMPsdegrade mainly type IV collagen and gelatin, and are distinguished bythe presence of an additional domain inserted into the catalytic domain.This gelatin-binding region is positioned immediately before the zincbinding motif, and forms a separate folding unit which does not disruptthe structure of the catalytic domain. This class includes MMP-2 (72 kDagelatinase, gelatinase-A); MMP-9 (92 kDa gelatinase, gelatinase-B).Finally, the membrane-bound MMPs are those that are attached to theouter cellular membrane. They include: The type-II transmembranecysteine array MMP-23; the glycosyl phosphatidylinositol-attached MMPs17 and 25 (MT4-MMP and MT6-MMP respectively); and the type-Itransmembrane MMPs 14, 15, 16, 24 (MT1-MMP, MT2-MMP, MT3-MMP, andMT5-MMP respectively). All of these MMPs have a furin cleavage site inthe pro-peptide, which is a feature also shared by MMP-11.

Thus, inhibiting the interaction of endosialin with an endosialin ligandinhibits the expression and/or activation of MMPs on theendosialin-expressing cell. In some preferred embodiments, theexpression or activation of MMP-1, MMP-2, MMP-8, MMP-9, MMP-12, MMP-13,or MMP-18 is suppressed by the inhibition.

Without intending to be bound to any particular theory or mechanism ofoperation, it is believed that endosialin functions directly orindirectly in angiogenesis, particularly with respect toneovascularization and diseases such as cancer. Therefore, it isbelieved that disrupting the binding of endosialin orendosialin-expressing cells to endosialin ligands, or disruptingendosialin-mediated activation of integrins, expression of MMPs and/orcellular proliferation/survival can suppress vascularization associatedwith neovascular disease.

Accordingly, the invention also features methods for inhibitingangiogenesis. The methods can be carried out in vitro or in vivo. In oneaspect, the methods for inhibiting angiogenesis comprise administeringto a subject a therapeutically effective amount of a composition thatobstructs endosialin expressed on the surface of a cell, wherein saidobstruction inhibits the interaction of said cell with a ligand forendosialin, and wherein the inhibiting of said interaction of said cellwith said ligand inhibits angiogenesis of a tissue, organ, or neoplasmin the subject.

In another aspect, the methods for inhibiting angiogenesis comprisecontacting a cell, cell culture, tissue, or organ with a compositionthat obstructs endosialin expressed on the surface of a cell, whereinsaid obstruction inhibits the interaction of said cell with a ligand forendosialin, and wherein the inhibiting of said interaction of said cellwith said ligand inhibits angiogenesis by said cell, cell culture,tissue, or organ.

In some preferred embodiments, the composition comprises at least onecompetitive inhibitor described herein. In some embodiments, thecompetitive inhibitors are endosialin ligands, for example, collagen,fibronectin, or endosialin-binding fragments thereof. Preferredcompetitive inhibitors are fragments of collagen I, collagen IV, orfibronectin. Most preferred competitive inhibitors are the 70 kDaN-terminal fragment of fibronectin, the 45 kDa gelatin binding fragmentof fibronectin, and the 30 kDa heparin binding fragment of fibronectin.

In preferred embodiments, the composition comprises at least oneantibody that specifically binds to endosialin. Such antibodiespreferably have an affinity for endosialin that is less than about1×10⁻⁷ M, more preferably less than about 1×10⁻⁸ M, more preferably lessthan about 1×10⁻⁹ M, and more preferably less than about 1×10⁻¹⁰ M.Antibodies that specifically bind to endosialin can include thoseantibodies whose characteristics are described and exemplified herein.For example, in some preferred aspects, the antibody that specificallybinds to endosialin comprises a heavy chain comprising CDR1, CDR2, andCDR3 of SEQ ID NO:28, 30, and 32, respectively, and a light chaincomprising CDR1, CDR2, and CDR3 of SEQ ID NO: 13, 15, and 17,respectively. In some embodiments, the heavy chain CDR1, CDR2, and CDR3are encoded by nucleotide sequences of SEQ ID NO:27, 29, and 31,respectively. In some embodiments, the light chain CDR1, CDR2, and CDR3are encoded by nucleotide sequences of SEQ ID NO:12, 14, and 16,respectively. In some embodiments, the antibodies can comprise a heavychain comprising a variable domain of SEQ ID NO: 34 and a light chaincomprising a variable domain of SEQ ID NO: 19. In some embodiments, theheavy chain variable domain is encoded by the nucleotide sequence of SEQID NO:33. In some embodiments, the light chain variable domain isencoded by the nucleotide sequence of SEQ ID NO:18. In some embodiments,the antibodies can comprise a heavy chain comprising the amino acidsequence of SEQ ID NO:22 or 26 and a light chain comprising the aminoacid sequence of SEQ ID NO:11. In some embodiments, the heavy chain isencoded by the nucleotide sequence of SEQ ID NO:21 or 25 and the lightchain is encoded by the nucleotide sequence of SEQ ID NO:10. In someembodiments, the antibodies comprise a heavy chain comprising SEQ IDNO:20 or 24 and a light chain comprising SEQ ID NO:9. In someembodiments, the antibodies comprise a heavy chain encoded by thenucleic acid sequence of SEQ ID NO:8 or 23. Antibodies can comprise alight chain encoded by the nucleic acid sequence that comprises SEQ IDNO:7. Antibody-producing cells producing antibodies that can be used inaccordance with the invention have been placed with the Amer. Type Cult.Coll. (10801 University Blvd., Manassas, Va. 20110-2209) on Apr. 24,2006 and on Mar. 11, 2008 and have been assigned Access. Nos. PTA-7554and PTA-9017, respectively. The antibodies can be polyclonal,monoclonal, antigen-binding fragments, chimeric, humanized, fully human,and the like as described herein.

Inhibiting the expression of endosialin inhibits the interaction ofendosialin with any endosialin ligand. Endosialin ligands includeextracellular matrix proteins such as fibronectin and collagen.

The invention also features methods for inhibiting neovascularization.The methods can be carried out in vitro or in vivo. In one aspect, themethods for inhibiting neovascularization comprise administering to asubject a therapeutically effective amount of a composition thatobstructs endosialin expressed on the surface of a cell, wherein saidobstruction inhibits the interaction of said cell with a ligand forendosialin, and wherein the inhibiting of said interaction of said cellwith said ligand inhibits neovascularization of a tissue, organ, orneoplasm in the subject.

In another aspect, the methods for inhibiting neovascularizationcomprise contacting a cell, cell culture, tissue, or organ with acomposition that obstructs endosialin expressed on the surface of acell, wherein said obstruction inhibits the interaction of said cellwith a ligand for endosialin, and wherein the inhibiting of saidinteraction of said cell with said ligand inhibits neovascularization ofsaid cell, cell culture, tissue, or organ.

In some preferred embodiments, the composition comprises at least onecompetitive inhibitor described herein. In some embodiments, thecompetitive inhibitors are endosialin ligands, for example, collagen,fibronectin, or endosialin-binding fragments thereof. Preferredcompetitive inhibitors are fragments of collagen I, collagen IV, orfibronectin. Most preferred competitive inhibitors are the 70 kDaN-terminal fragment of fibronectin, the 45 kDa gelatin binding fragmentof fibronectin, and the 30 kDa heparin binding fragment of fibronectin.

In preferred embodiments, the composition comprises at least oneantibody that specifically binds to endosialin. Such antibodiespreferably have an affinity for endosialin that is less than about1×10⁻⁷ M, more preferably less than about 1×10⁻⁸ M, more preferably lessthan about 1×10⁻⁹ M, and more preferably less than about 1×10⁻¹⁰ M.Antibodies that specifically bind to endosialin can include thoseantibodies whose characteristics are described and exemplified herein.For example, in some preferred aspects, the antibody that specificallybinds to endosialin comprises a heavy chain comprising CDR1, CDR2, andCDR3 of SEQ ID NO:28, 30, and 32, respectively, and a light chaincomprising CDR1, CDR2, and CDR3 of SEQ ID NO: 13, 15, and 17,respectively. In some embodiments, the heavy chain CDR1, CDR2, and CDR3are encoded by nucleotide sequences of SEQ ID NO:27, 29, and 31,respectively. In some embodiments, the light chain CDR1, CDR2, and CDR3are encoded by nucleotide sequences of SEQ ID NO:12, 14, and 16,respectively. In some embodiments, the antibodies can comprise a heavychain comprising a variable domain of SEQ ID NO: 34 and a light chaincomprising a variable domain of SEQ ID NO: 19. In some embodiments, theheavy chain variable domain is encoded by the nucleotide sequence of SEQID NO:33. In some embodiments, the light chain variable domain isencoded by the nucleotide sequence of SEQ ID NO:18. In some embodiments,the antibodies can comprise a heavy chain comprising the amino acidsequence of SEQ ID NO:22 or 26 and a light chain comprising the aminoacid sequence of SEQ ID NO:11. In some embodiments, the heavy chain isencoded by the nucleotide sequence of SEQ ID NO:21 or 25 and the lightchain is encoded by the nucleotide sequence of SEQ ID NO:10. In someembodiments, the antibodies comprise a heavy chain comprising SEQ IDNO:20 or 24 and a light chain comprising SEQ ID NO:9. In someembodiments, the antibodies comprise a heavy chain encoded by thenucleic acid sequence of SEQ ID NO:8 or 23. Antibodies can comprise alight chain encoded by the nucleic acid sequence that comprises SEQ IDNO:7. Antibody-producing cells producing antibodies that can be used inaccordance with the invention have been placed with the Amer. Type Cult.Coll. (10801 University Blvd., Manassas, Va. 20110-2209) on Apr. 24,2006 and Mar. 11, 2008 and have been assigned Access. No. PTA-7554 andAccess. No. PTA-9017, respectively. The antibodies can be polyclonal,monoclonal, antigen-binding fragments, chimeric, humanized, fully human,and the like as described herein.

Inhibiting the expression of endosialin inhibits the interaction ofendosialin with any endosialin ligand. Endosialin ligands includeextracellular matrix proteins such as fibronectin, for example, humanfibronectin (SEQ ID NO:35) and collagen.

The invention also features assays and methods for identifying agonistsand antagonists of the interaction of endosialin with a ligand forendosialin. In some embodiments, the methods comprise contactingendosialin with a test compound, contacting the endosialin-test compoundcomplex with a ligand for endosialin, and quantifiably measuring theinteraction of endosialin with the ligand in the presence and in theabsence of the test compound. An increase or decrease in the level ofinteraction of endosialin with ligand in the presence of the testcompound indicates that the test compound is an agonist or antagonist,respectively, of the interaction of endosialin with the ligand.

In some embodiments, the methods comprise contacting anendosialin-expressing cell with a test compound, contacting theendosialin expressing cell with a ligand for endosialin, andquantifiably measuring the expression or activation of integrinmolecules such as integrin β1, β2, or β3 on the cell in the presence andin the absence of the test compound. An increase or decrease in thelevel of expression or activation of the integrin molecules on the cellin the presence of the test compound indicates that the test compound isan agonist or antagonist, respectively, of the interaction of endosialinwith said ligand.

In some embodiments, the methods comprise contacting anendosialin-expressing cell with a test compound, contacting theendosialin expressing cell with a ligand for endosialin, andquantifiably measuring the expression or activation of MMPs such asMMP-1, MMP-2, MMP-8, MMP-9, MMP-12, MMP-13, or MMP-18 on the cell in thepresence and in the absence of the test compound. An increase ordecrease in the level of expression or activation of the MMP moleculeson the cell in the presence of the test compound indicates that the testcompound is an agonist or antagonist, respectively, of the interactionof endosialin with said ligand.

In the inventive assays, the endosialin can be bound to a cell membrane,preferably a mammalian cell membrane, a cell membrane fragment, anartificial lipid bilayer, or to a suitable solid support. The endosialinligand can be an extracellular matrix protein, including withoutlimitation fibronectin or collagen.

One strategy for generating test compounds with potential biologicactivity against endosialin or endosialin-expressing cells, i.e.,potential interaction with endosialin, involves but is not limited toscreening phage libraries producing phage coat peptides that can bescreened to identify polypeptides in a library that can potentiallyserve to inhibit the interaction between endosialin and an endosialinligand.

The following examples are provided to describe the invention in greaterdetail. They are intended to illustrate, not to limit, the invention.

Example 1 Immunohistochemistry Analysis of Endosialin Expression onMalignant Tissue

Use of antibodies to detect endosialin-expressing cells was shown byimmunohistochemistry of malignant tissues. The anti-endosialin or normalIgG antibody was applied to freshly frozen human colorectal cancertissues at two concentrations (0.5 μg/mL and 2.5 μg/mL).Phosphate-buffered saline [PBS (0.15M NaCl, pH 7.2)]+1% bovine serumalbumin served as the diluent for the primary antibodies. Tissues wereembedded in Tissue-Tek® O.C.T. medium, frozen on dry ice, and stored insealed plastic bags below −70° C. Tissues were sectioned atapproximately 5 μm, and fixed for 10 minutes in room temperatureacetone. Slides were stored below −70° C. until staining Just prior tostaining, slides were fixed for 10 seconds in 10% neutral-bufferedformalin.

Cryosections were rinsed twice in phosphate-buffered saline (PBS [0.15MNaCl, pH 7.2]). Endogenous peroxidase was blocked by incubating theslides with the peroxidase solution provided in the Dako EnVision™ Kitfor 5 minutes and rinsing twice in PBS (0.15M NaCl, pH 7.2). Next, theslides were treated with a protein block designed to reduce nonspecificbinding for 20 minutes. The protein block was prepared as follows: PBS(0.15M NaCl, pH 7.2); 0.5% casein; 1% bovine serum albumin (BSA); and1.5% normal goat serum. Following the protein block, the primaryantibody (test article M4, negative control antibody, or none [bufferalone as the assay control]) was applied at room temperature for onehour. Next, the slides were rinsed two times with PBS (0.15M NaCl, pH7.2), treated with the peroxidase-labeled goat anti-IgG polymer suppliedin the Dako EnVision™ Kit for 30 minutes (EnVision™ polymer used at theconcentration provided by manufacturer), rinsed two times with PBS(0.15M NaCl, pH 7.2), and treated with the substrate-chromogen (DAB)solution supplied in the Dako EnVision™ Kit for 8 minutes. All slideswere rinsed in water, counterstained with hematoxylin, dehydrated andcoverslipped for interpretation. As shown, vessels in the tumor (FIG.1A) stained positive for endosialin while isotype control antibodystained serial section was negative (FIG. 1B).

Example 2 Immunohistochemistry Analysis of Endosialin Expression onHealthy Tissue

Use of antibodies to detect endosialin-expressing cells was shown byimmunohistochemistry of normal tissues. Briefly, normal tissue specimenswere sectioned by cryostat and analyzed for endosialin expression asdescribed above. Normal tissues contained very fewfibroblast/dendritic-like cells that expressed endosialin albeit not asrobustly or homogenously as was observed in the vessels within tumors(FIGS. 2A and B). These cells are useful to study the effects ofneovascularization and can be isolated for gene expression to studyprofiles of cell growth, differentiation, migration or signatureidentification. They can be studied in vivo, ex vivo or in vitro usingmethods known by those skilled in the art as well as those listed below.

Example 3 Isolation and Enrichment of Endosialin-Expressing Cells

To demonstrate that proteins that can bind to endosialin serve as aneffective way to enrich for endothelial or fibroblast-likeendosialin-expressing cells, Human Microvascular Endothelial Cells(HMVECs) were panned using an antibody that can bind to endosialin toisolate an enriched population of endosialin-expressing cells from astarting pool containing 5-10% endosialin-expressing cells. Not wantingto be bound by the method or specific reagents below, this exampledemonstrates the use of endosialin antibodies that can isolateendosialin expressing cells.

Briefly, 96-well plates were coated in sterile conditions with goat antihuman IgG Fcγ. Next, 20 μg/ml of a human anti-endosialin antibody M4 wasadded to the plates and three wells (A, B, C) as controls without theantibody and incubated for 1 hr at 4° C. HMVECs were harvested from 10cm petri dish cultures with DPBS/EDTA rather than trypsin to avoid anydamage to the cell membranes, thereby leaving the endosialin cellsurface proteins intact. Pooled cells were plated at two differentconcentrations, either 100,000 cells/well or 50,000 cells/well in the96-well plates after aspirating and washing off any unboundanti-endosialin antibody. Cells were incubated in plates for one hour at4° C. Plates were then washed with DPBS/FBS four times (until controlwells A, B, and C showed no cells within the wells). The 50,000cells/well plate showed very few cells while the 100,000 cells/wellwells contained a number of cells attached to plate. Cells were thenincubated for three days in appropriate growth media. The control B andC wells were picked from the 100,000 cells/well plates forimmunostaining Calcein, AM dye was used to stain the cells forvisualization using a Nikon® Eclipse TS100 Fluorescence Microscope.Positive panned cultures were expanded for growth and further analysisfor homogeneous endosialin expression as described below.

To further determine the ability to isolate endosialin-expressing cells,anti-endosialin-antibody panned HMVEC cells and non-panned HMVECcultures were prepared for immunostaining using a fluorescentanti-endosialin antibody or fluorescent α-β1-integrin antibody ascontrol. As expected, greater than 90% of the cells stained positive forα-β1-integrin from panned and non-panned cultures (not shown), whilegreater than 90% of cells stained positive for endosialin from pannedcultures while only 5-7% of cells stained positive for endosialin inunpanned HMVEC cultures. These data demonstrate the ability to isolateand enrich viable endosialin-expressing cells using endosialin-bindingproteins such as antibodies.

As shown in FIG. 3, the panned culture had a much higher number ofendosialin-positive cells as compared to the non-panned parental cultureas determined by immunostaining via anti-endosialin antibody followed bya fluorescent conjugated secondary antibody. Cell number of each fieldwas determined by light microscopy.

Example 4 Endosialin Interaction with Extracellular Matrix Proteins

Construction of TEM1 and Fc-TEM-1 Expression Plasmids.

PCR was used to amplify a DNA fragment representing amino acids 1-685 ofthe TEM1 open reading frame (GenBank #AF279142) from LA1-5S genomic DNA.The resulting amplicons were digested with EcoRI and XbaI and ligatedinto pEF6-V5-HisA (Invitrogen). To generate Fc-TEM-1, the extracellularregion of TEM1 was fused to monomeric murine IgG2_(b) Fc_(γ) domain andligated into the derivative pEF6-EK-Mm-IgG2b-Fcγ-ND vector whichcontains an enterokinase recognition region (DDDD) followed by amodified murine IgG2_(b) Fc_(γ) (hinge through CH3) domain. To preventdimerization, the four cysteine residues responsible for inter-heavychain disulfide bonding were changed to serine. The resulting monomeric,secreted fusion protein consists of the full-length TEM1 extracellulardomain and the murine IgG2_(b) Fc_(γ). The integrity of all plasmidsequences was verified using Beckman® DTCS chemistry (Beckman Coulter,Fullerton, Calif.). Raw data were acquired with a CEQ 8000 DNA sequencerand analyzed using Vector NTI® software (Invitrogen).

Purification of Fc-TEM-1.

CHO-TEM1-Fcγ cells were cultured at 25 L scale in IS-CHO-CD medium(Irvine Scientific, Santa Ana, Calif.), supplemented with 2 mML-glutamine, 1× Penicillin/Streptomycin, 6 g/L soybean hydrolysate and2.2 g/L sodium bicarbonate (Irvine Scientific), on a Wave20/50EHplatform fitted with a Cellbag50® (GE Healthcare, Piscataway, N.J.),until the viability of the culture reached 50-70%. Conditionedextra-cellular medium was clarified using a Flexstand® Benchtop PilotHollow Fiber System (GE Healthcare) equipped with a 0.2 μm hollow fibercartridge (GE Healthcare) until 0.5 L of culture remained in the holdingvessel. At this point, the concentrated cell mass was washed with 4 L ofphosphate-buffered saline (PBS, 20 mM K Phosphate, 150 mM NaCl pH 7.2),to recover remaining extra-cellular fluid. The 4 L wash was pooled withthe clarified feedstock. The clarified culture medium was thenconcentrated twelve-fold (29 L to 2.5 L); using a Prep/Scale® SpiralWound 2.5 ft² 100 k ultrafiltration cartridge set in a Prep/Scale®holder (Millipore, Billerica, Mass.), and driven by a peristaltic pumpat an inlet pressure of 20 PSI, and a recirculation rate ofapproximately 400 mL/min. The resulting concentrated feedstock wasfilter-sterilized through bottle top filters equipped with a 0.2 μmmembrane (Nalgene). TEM1-Fcγ was captured by protein A affinitychromatography, over a 10×100 mm ProSep-vA® (Millipore) column, andeluted by addition of 5 column volumes of elution buffer (100 mMcitrate/10 mM acetate pH 3.0). Eluted material was dialyzed againstbuffer QA (20 mM Tris-Cl pH 8.0), and further purified by ion-exchangechromatography over a 5 mL HiTrap® Q-FF column (GE Healthcare). Boundproteins were washed with 15% buffer QB (20 mM Tris-Cl, 1 M NaCl pH8.0), followed by elution of bound Fc-TEM-1 using 35% buffer QB. Elutedproteins were concentrated by ultra-filtration in a Model 8400 positivepressure ultra-filtration module (Millipore) fitted with a 100 kDa MWCOmembrane (Millipore), to a final volume of approximately 5 mL.Concentrated Fc-TEM-1 was purified by preparative size exclusionchromatography on a Sephacryl® S-300HR 26×60 column (GE Healthcare),equilibrated with PBS. Fractions containing purified Fc-TEM-1 werepooled, concentrated to a nominal range between 0.1-1 mg/mL byultra-filtration using a 100 kDa MWCO membrane and stored in single-usealiquots at −80° C.

Purified Fc-TEM-1 (2.9 μg) was loaded onto a 4-12% Bis-Tris gel(Invitrogen, Inc.), and electrophoresed in MOPS Running Buffer (50 mMMOPS, 50 mM Tris, 3.5 mM SDS, 1 mM EDTA pH 7.7), for 40 minutes. Forstaining, the gel was fixed for 15 minutes in Fix solution (50%methanol, 10% acetic acid), washed twice for 10 minutes in deionizedwater, and stained for at least one hour using GelCode Blue colloidalCoomassie Blue stain (Pierce). The gel was de-stained by repeatedwashing with deionized water.

Pre-coated Fibronectin (FN), Collagen I (Col I), Collagen IV (Col IV),Laminin (LN) (BD Biosciences, San Diego Calif.), Vitronectin (VN), orGelatin (Gel) (Chemicon Intl.) 96-well plates were used to assessFc-TEM-1 binding. The binding of TEM1 to Col I, Col IV, and FN was notdue to trace contaminants in the purified protein from human plasmasince neither Col I nor Col IV was detected in FN by anti-Col antibodyELISA, nor was FN detected in Col (data not shown). All plates wereblocked with assay buffer (0.5% BSA, 0.5% Tween-20 in PBS) for 2 h priorto the addition of Fc-TEM-1 fusion protein, a soluble endosialingenerated by fusion of the N-terminal leader sequence and the entireextracellular domain of endosialin to a murine gamma heavy chain.Following 1 h incubation at room temperature, the plates were washed andthe HRP-goat anti-human IgG (H+L) antibody (Jackson ImmunoresearchLaboratories, West Grove, Pa.) was added for 1 h. Color development wasassessed using the SureBlue™ TMB Peroxidase Substrate (KPL,Gaithersburg, Md.). Both BSA and a human isotype control antibody wereused as negative controls. Fc-TEM-1 did not bind BSA, nor did the humanisotype bind any of the ECM proteins (data not shown).

As shown in FIG. 4A, the Fc-TEM1 bound to fibronectin and collagen I andIV in a dose dependent manner while no binding was observed within theentire dose range to LN or VN. Interestingly, while Fc-TEM1 boundcollagen, no detectable binding to gelatin (heat-denatured collagen) wasobserved. None of four murine isotype IgG antibodies tested could bindto any of the ECM proteins, ruling out the possibility that theinteractions were mediated by murine Fc backbone of the Fc-TEM1 fusionprotein (data not shown). A fusion protein containing the murine gammaheavy chain and only the lectin domain of endosialin also binds FN (datanot shown).

To confirm selectivity of the Fc-TEM1 and ECM protein interaction,Fc-TEM1 was applied to ELISA plates coated with different purifiedproteins. Antigen-specific ELISAs were performed by coating TPImmunomini ELISA plates with 1 ug/ml STEB (Staphylococcus enterotoxin Bvaccine), 2 ug/ml bovine gamma globulin, 2 ug/ml tumor-associated 90 kDglycoprotein antigen expressed on most melanoma cells (TA90), 2 ug/mlhen egg lysozyme, 1:500 dilution of tetanus toxoid, 1% BSA, 0.2 ug/mlhuman mesothelin, 2 ug/ml ovalbumin (OVA), 1 ug/ml human GM-CSF, 2 ug/mlgoat IgG, 2 ug/ml mouse IgG dissolved in bicarbonate coating buffer (pH9.6) (Sigma) overnight at 4° C. The plates were washed three times withwashing buffer (containing 0.5% TWEEN-20) blocked with 1× assay bufferfor 2 hours at room temperature and ELISA was performed as describedabove. As shown in FIG. 4B, Fc-TEM1 did not bind to any of the proteinstested except for the anti-mouse Fc used as a positive control.

Example 5 Inhibition of TEM1 Binding to Human Plasma Fibronectin

96-well plates were pre-coated with Fibronectin (FN), and the ability ofanti-TEM-1 antibodies to block Fc-TEM-1 mediated adhesion was assessedby ELISA. Briefly, the FN-coated plate was blocked with assay buffer(0.5% BSA, 0.5% Tween-20 in PBS) for 2 h prior to the addition of fusionproteins. Fc-TEM-1 was pre-incubated for 1 h at 4° C. with theantibodies M4 (a humanized anti-endosialin antibody described as ES1 inU.S. Pat. Publication No. 20060239911), human isotype (HuIgG), oranti-TEM-1 antibody raised in rabbits (RbtTEM1). M4 does not bind tospecies homologs of endosialin with the exception of nonhuman primates.The binding epitope for M4 has been mapped to the extracellular lectindomain of endosialin. The protein/antibody complex was added to theFN-coated plate and allowed to adhere for 1 h at room temperature atwhich time the plates were washed and the HRP-goat anti-human IgG (H+L)antibody (Jackson Immunoresearch Laboratories, West Grove, Pa.) wasadded for 1 h. Color development was assessed using the SureBlue™ TMBPeroxidase Substrate (KPL, Gaithersburg, Md.). As shown in FIG. 6, M4suppressed Fc-TEM1 binding to fibronectin, whereas a non-specificcontrol (HuIgG) did not suppress binding. RbtTEM1 also suppressedFc-TEM1 binding to fibronectin (data not shown).

Example 6 Endosialin Mediates Adhesion to Fibronectin

CHO-TEM1 cells stably expressing endosialin (verified by FACS with M4antibody; data not shown) were generated. CHO-K1 cells were maintainedin RPMI supplemented with L-glutamine, 1% minimal essential amino acids,Sodium pyruvate, Non-Essential amino acids, and 10% heat-inactivated FBS(Invitrogen, Carlsbad, Calif.). CHO-K1 cells (3E6) (ATCC, Manassas, Va.)were electroporated with 10 ug linearized plasmid DNA in a 0.4 mmelectroporation cuvette. A pulse of 170V/1000 uF was delivered using aGENE PULSER (BioRad, Hercules, Calif.). Electroporated cells wereallowed to recover for 24 hours after which Blasticidin (5ug/ml)-resistant clones were selected. Endosialin expression wasverified by FACS and cells were sorted for high expression.

Cells (1.5×10⁵ cells/well) were washed and suspended in PBS containingMg²⁺/Ca²⁺, and added in quadruplicate to a 96-well-plate coated withFibronectin and allowed to adhere for 1 h. Where indicated, cells werepre-incubated with antibody (100 ug/mL) M4 or human isotype (IgG) for 1h prior to the start of the assays. After the cells were allowed toadhere the plate was washed 5 times with PBS and viability was measuredusing CellTiter-Glo® (Promega, Madison, Wis.). FIG. 9B shows thatover-expression of endosialin results in increased cell binding tofibronectin, which can be blocked by endosialin inhibitors such asantibody M4, in contrast to controls such as nonspecific IgG.

Example 7 Endosialin Binding to Fibronectin and Fibronectin Fragments

Fibronectin is a large complex glycoprotein that exists as a dimercovalently linked by a disulfide bridge at the C-terminus of the protein(Ruoslahti et al. (1981) J. Biol. Chem., 256:7277-7281;Wierzbicka-Patynowski & Schwarzbauer (2003) J. Cell Sci., 116:3269-3276;Magnusson & Mosher (1998) Arterioscler. Thromb. Vasc. Biol.,18:1363-1370). Fibronectin fragments either derived from enzymaticdegradation or alternative splicing have been reported to be associatedwith certain disease states and possess distinct biological functions(Magnusson & Mosher (1998) Arterioscler. Thromb. Vasc. Biol.,18:1363-1370; Labat-Robert (2002) Semin. Cancer Biol., 12:187-195;Homandberg (1999) Front Biosci., 4:D713-730).

The ability of Fc-TEM-1 to bind to different fibronectin fragments wasassessed. Equimolar amounts of proteins were diluted in coating buffer(50 mM Carbonate-bicarbonate, pH9.4), added to an ELISA plate (GreinerBio-one, Monroe, N.C.) and incubated overnight at 4° C. All plates wereblocked with assay buffer (0.5% BSA, 0.5% Tween-20 in PBS) for 2 h priorto the addition of Fc-TEM-1. Following 1 h incubation at roomtemperature, the plates were washed and the HRP-goat anti-human IgG(H+L) antibody (Jackson Immunoresearch Laboratories, West Grove, Pa.)was added for 1 h. Color development was assessed using the SureBlue™TMB Peroxidase Substrate (KPL, Gaithersburg, Md.). To assess theintegrity of coated fibronectin proteins, the rabbit polyclonal antibodydirected against fibronectin (FN Ab) was used to detect that all FNfragments were recognizable and coated evenly.

The full length human plasma purified Fibronectin and 120 kDa cellattachment FN-fragment proteins were purchased from Chemicon Intl.(Temucula, Calif.), proteolytic 30 kDa, 45 kDa, 70 kDa fragments fromSigma (St. Louis, Mo.), and the recombinant human fibronectin fragments2 and 4 (FN2 and FN4, respectively) from R&D Systems (Minneapolis,Minn.).

As shown in FIG. 7A, Fc-TEM1 binds the amino terminal 70 kDa fragment ofFN and its proteolytic cleavage products (45 kDa and 30 kDa fragments).The extent of binding varied among the different fragments and was lessthan that seen with whole FN. In contrast, Fc-TEM1 did not bind the 120kDa FN fragment or the recombinant fragments Fn2 or Fn4. This lack ofbinding was unlikely due to uneven coating or degradation since all FNfragments were strongly detected by an anti-FN polyclonal antibody. Thisis evidence that the FN domain involved in interaction with endosialinresides within the 70 kDa amino terminal portion. To determine whetherthe reduced binding capacity upon further digestion of the 70 kDafragment indicates that Fc-TEM1 binds to a region located in closeproximity to the proteolytic cleavage site or that TEM1 recognizesconformationally dependent epitopes within the amino terminus of FN thatis altered after further digestion, the ability of Fc-TEM1 to bindreduced forms of FN proteins was examined. While anti-FN antibody wasable to recognize reduced FN, indicating equivalent coating, the bindingof Fc-TEM1 was completely ablated as shown in FIG. 7B. Similar to wholeFN, anti-endosialin antibody M4 blocked Fc-TEM1 binding to the 70 kDafragment in a dose-dependent manner (FIG. 7C), while an isotype controlantibody had no effect (FIG. 7D). These results indicate that Fc-TEM1recognizes conformationally dependent epitopes located within the aminoterminus of FN that can be impaired upon further proteolyticdegradation.

Example 8 Association of Cell Surface Fibronectin with Endosialin

CHO-TEM1 cells stably expressing endosialin (verified by FACS with M4antibody; data not shown) were generated. CHO-K1 cells were maintainedin RPMI supplemented with L-glutamine, 1% minimal essential amino acids,Sodium pyruvate, Non-Essential amino acids, and 10% heat-inactivated FBS(Invitrogen, Carlsbad, Calif.). CHO-K1 cells (3E6) (ATCC, Manassas, Va.)were electroporated with 10 ug linearized plasmid DNA in a 0.4 mmelectroporation cuvette. A pulse of 170V/1000 uF was delivered using aGENE PULSER (BioRad, Hercules, Calif.). Electroporated cells wereallowed to recover for 24 hours after which Blasticidin (5ug/ml)-resistant clones were selected. Endosialin expression wasverified by FACS and cells were sorted for high expression.

The level of cell surface FN was examined by flow cytometry in parentalCHO-K1 and CHO-TEM1 cells using a polyclonal anti-FN antibody. Cellswere harvested in Cell Dissociation Buffer (Invitrogen, Carlsbad,Calif.), washed, and resuspended in ice-cold PBS+1% FBS. Cells wereincubated for 1 hour on ice with primary antibody, M4 (10 ug/ml),washed, and incubated with FITC-conjugated goat-anti-human secondaryantibody (Southern Biotech, Birmingham, Ala.) and analyzed on anEASYCYTE Flow Cytometer (Guava Technologies, Hayward, Calif.). 15-20%higher levels of surface FN in CHO-TEM1 cells compared to CHO-K1 cellswere observed constantly (data not shown). Association of cell surfaceFN with endosialin was examined.

Using an anti-FN antibody, FN was immunoprecipitated from both CHO-K1and CHO-TEM1 lysates, followed by Western blot using the same antibodyor an anti-TEM1 antibody (M4). Cells (10E7) were lysed inradioimmunoprecipiation (RIPA) buffer (50 mM Tris-HCl, pH 7.4, 1% NP-40,0.5% sodium deoxycholate, 150 mM NaCl, 0.1% sodium dodecyl sulfate[SDS]) supplemented with Complete Mini Protease Inhibitor Cocktail(Roche Diagnostics, Indianapolis, Ind.) and centrifuged at 13,000 rpmfor 15 min to remove debris. Protein G Sepharose 6 Fast Flow Beads(Amersham Biosciences, Piscataway, N.J.) were washed 3 times with PBSand anti-FN antibody (1 ug) was captured by gentle rocking at 4° C.Equal amounts of protein per sample were pre-cleared by the addition ofunbound Protein G. After 2 hours of incubation, the Protein G wasremoved and the supernatant was added to the antibody-Sepharose complexand incubated overnight at 4° C. After extensive washing with RIPAbuffer, the bound protein was removed by boiling for 10 minutes inNuPAGE® LDS sample buffer (Invitrogen) containing 5% β-mercaptoethanol.Proteins were separated using SDS-polyacrylamide gel electrophoresis ona 4-12% Bis-Tris gel (Invitrogen) and transferred to PVDF membrane.Immunoblotting was conducted using rabbit polyclonal antibodies specificfor fibronectin (Abcam, Cambridge, Mass.) or endosialin (Morphotek,Inc., Exton, Pa.), detected with a goat-anti-rabbit HRP-conjugatedantibody, and visualized using SUPERSIGNAL West Pico chemiluminescentsubstrate (Pierce, Rockford, Ill.). The integrity and purity of solubleFc-TEM1 was also monitored by Western blot. Protein (5 ug) was boiledfor 5 min in 4× NUPAGE LDS Sample Buffer (Invitrogen) containing 5%β-mercaptoethanol, subjected to electrophoresis on a NUPAGE 4-12%Bis-Tris gel (Invitrogen), and transferred to PVDF membrane andimmunoblotting was performed as described above.

It was found that FN can immunoprecipitate endosialin from CHO-TEM1lysates (data not shown). In contrast, in cell lysatesimmunoprecipitated with a normal IgG that did not pull down FN, noendosialin could be detected (data not shown). At least two differentapproaches (ELISA and coimmunoprecipitation) provide strong evidence ofFN and endosialin interaction. Similar results were obtained usingHEK-293T cells ectopically expressing endosialin (data not shown).

Example 9 Cells Expressing Endosialin Cultured on MATRIGEL Form Web-LikeStructures

While no differences in growth or survival were observed betweenparental CHO-K1 and CHO-TEM1 cells cultured on plastic surface, adrastically different morphology was observed when these cells werecultured on MATRIGEL. Parental CHO-K1 cells grew into isolated cellclusters with minimal protrusions after 2 days of culturing (FIG. 8, toppanels), while CHO-TEM1 cells grew into clusters forming a web-likenetwork (FIG. 8, bottom left panel). In addition, CHO-TEM1 cells withinthe cluster exhibited protrusions reaching out to other clusters (FIG.8, bottom right panel). Over time, CHO-TEM1 cells but not CHO-K1 cellsmoved closer to each other to form larger clusters (data not shown).

Example 10 Endosialin Expression Increases Cell Adhesion to Fibronectin,and the 70 kD or 30 kD N-Terminus of Fibronectin

To assess adhesion to FN fragments, equimolar amounts of proteinfragments were pre-coated overnight and then blocked for 2 h with PBScontaining 10 mg/mL BSA. MATRIGEL served as a positive control. CHO-K1or CHO-TEM1 cells (1.5×10⁵ cells/well) harvested in cell dissociationbuffer were washed and suspended in PBS containing Mg²⁺/Ca²⁺, and addedin quadruplicate to an ECM Cell Adhesion Array Kit (Millipore) or platedon individually coated FN, LN, Gel, and Col I plates (BD Biosciences)and allowed to adhere for 1 h. Following incubation, each well waswashed 5 times with PBS and viability was measured using CellTiter-Glo®.Where indicated, cells were pre-incubated with antibody for 1 hour priorto the start of the assay. As shown in FIG. 9A, the number of adherentCHO-TEM1 cells was 6-fold higher than the number of parental CHO-K1cells in wells coated with FN. No significant differences in adhesionbetween CHO-K1 and CHO-TEM1 on surfaces coated with laminin orvitronectin were observed, while adhesion to collagens and tenascin wastoo weak to assess any valuable differences (FIG. 9A). Pretreatment ofCHO-TEM1 cells with M4 antibody resulted in 50% reduction ofTEM1-FN-dependent cell adhesion, while IgG control antibody had noeffect (FIG. 9B). M4 antibody treatment did not affect FN-dependent,endosialin-independent cell adhesion (baseline adhesion) of parentalCHO-K1 cells.

Plates were precoated with equimolar amounts of whole FN, FN proteolyticfragments, and MATRIGEL. CHO-TEM1 cells showed a 3- to 5-fold increasedadhesion to FN, 70 kDa, and 30 kDa fragments compared to parental CHO-K1cells, whereas no significant adhesion was seen to 45 kDa or Fn2fragments. CHO-TEM1 cells bound MATRIGEL five times better than CHO-K1(FIG. 9C). These data indicate that endosialin enhances the adhesion ofcells to extracellular matrices and that the amino terminus of FN isinvolved with these interactions.

Example 11 Endosialin Binds to Collagen I and M4 Inhibits this Binding

A 96-well plate pre-coated with Collagen I was used to assess M4 abilityto block Fc-TEM-1 binding. The plate was blocked with assay buffer (0.5%BSA, 0.5% Tween-20 in PBS) for 2 h prior to the addition of protein atthe indicated concentration (μg/mL). Fc-TEM-1 was pre-incubated for 1 hat 4 C with the antibodies M4 or human isotype (Human IgG). Theprotein/antibody complex was then added to the Col I-coated plate andallowed to adhere for 1 h at room temperature at which time the plateswere washed and the HRP-goat anti-human IgG (H+L) antibody (JacksonImmunoresearch Laboratories, West Grove, Pa.) was added for 1 h. Colordevelopment was assessed using the SureBlue™ TMB Peroxidase Substrate(KPL, Gaithersburg, Md.). As shown in FIG. 10, over-expression ofendosialin results in increased cell binding to COL I, which can beblocked by endosialin inhibitors such as M4, in contrast to controlssuch as nonspecific IgG. RbtTEM1 also suppressed Fc-TEM1 binding to ColI (data not shown).

Example 12 Endosialin Increases Cell Adhesion to Collagen

CHO-K1 or CHO-TEM1 cells (1.5×10⁵ cells/well) were washed and suspendedin PBS containing Mg²⁺/Ca²⁺, and added in quadruplicate to a 96-wellplate coated with Collagen I and allowed to adhere for the indicatedtime points. After the cells were allowed to adhere the plate was washed5 times with PBS and viability was measured using CellTiter-Glo®. Asshown in FIG. 11, over-expression of endosialin results in increasedcell binding to COL I.

Example 13 Cell Migration Assay

The BD BioCoat Tumor Invasion System™ (BD Bioscience) and HumanFibronectin Cell Culture inserts (BD Bioscience) were used to assessTEM1-mediated migration of cells. Cells were harvested with nonenzymaticcell dissociation buffer and diluted to a concentration of 4E5 cells/mlin growth media supplemented with 2% fetal bovine serum (FBS), and 500ul of cell suspension was added to the top chamber of the membraneinsert. To create a gradient, growth media containing 20% FBS was addedto the bottom chamber. Cells were incubated for 48 hours, after whichthe insert was removed and cells that had migrated through the coatedmembrane were counted using CELLTITER-GLO (Promega). Cells werepretreated with antibody as indicated in the description of FIG. 12 andmigration was assessed in the continual presence of antibody. To examinethe formation of tubules on MATRIGEL, cells (8E4 cells/well) were addedto a 96-well plate coated with MATRIGEL (BD Bioscience), incubatedovernight and photographed at 200-400× magnification.

As shown in FIG. 12A, CHO-K1 cells exhibited modest cell migration,whereas CHO-TEM1 cells showed >10-fold enhanced migration. M4 antibodytreatment, but not control IgG, abolished CHO-TEM1 cell migration.Similar results were observed in migration experiments using transwellchambers coated with FN (FIG. 12B).

Example 14 Endosialin Increases MMP-9 Activity

Endosialin, MMP-2, and COL IV have been shown to colocalize in tissueareas characterized by finger-like protrusions of early angiogenicprocesses (Virgintino et al. (2007) Angiogenesis, 10:35-45). To assessMMP activity, cells were seeded in a 6-well plate and serum starved for48 h. The culture supernatant was collected and clarified bycentrifugation (13,000 rpm, 15 min.) at 4° C. to remove any debris.Equal amounts of protein were subjected to gelatin and casein zymographyunder nonreducing conditions (Invitrogen) according to themanufacturer's protocol. Positive controls human MMP-2 and 9 (Chemicon,International) were used to indicate the migration of MMP-2 and MMP-9and used as a reference for our CHOK1 and CHO-TEM-1 supernatants. Asshown in FIG. 13, MMP-9 activity was significantly enhanced in CHO-TEM1cells compared to parental CHO-K1 cells. The enhanced MMP-9 activitycorrelated with increased secretion of MMP-9 protein in the supernatantof CHO-TEM1 cells as measured by a MMP-specific ELISA (data not shown).These data indicate that induced MMP-9 secretion contributes to theenhanced migration capability of CHO-TEM1 cells through MATRIGEL andFN-coated transwells demonstrated herein.

Example 15 Endosialin Increases β-Integrin Activity

Integrins (e.g., α4β1, α5β1) are well-characterized receptors thatmediate FN-dependent cell adhesion (Wierzbicka-Patynowski & Schwarzbauer2003; Magnusson & Mosher 1998). In addition, an unidentified cellularreceptor has been functionally described that binds the N-terminal 70kDa region of FN (McKeown-Longo & Mosher (1983) J. Cell Biol.,97:466-472) and is required to expose the cryptic integrin-binding site(RGD motif) of soluble FN involved with FN-integrin and FN-FNinteractions (Tomasini-Johansson et al. (2006) Matrix Biol., 25:282-293;McKeown-Longo & Mosher (1985) J. Cell Biol., 100:364-374). Endosialin isidentified herein as a novel receptor that interacts with the N-terminal70 kDa FN region and enhances FN-dependent cell adhesion. The enhancedFN binding measured in these cellular systems in vitro could be theresult of sequential interaction with endosialin and integrins.

Human embryonic kidney 293 (HEK293) cells were transfected with a vectorexpressing endosialin or mock cDNA. Cells were confirmed to express cellsurface endosialin (293TEM1) while those transfected with mock (293T)did not. Cells were the tested for the ability to upregulate integrinexpression and activity in the presence of antibody M4. FIG. 14B showsthat over-expression of endosialin results in increased integrin β1activity relative to control cells. FIG. 14A shows that cell surfaceintegrin β1 expression is not changed. Treatment of cells with theendosialin inhibitor M4 resulted in suppressed integrin activity whileno effect on cell surface levels were observed (FIG. 14B). While notwishing to be bound to any one theory, the interaction betweenendosialin and the N-terminal 70 kDa fragment of soluble FN may beresponsible for initiating the assembly of FN into a multimeric highaffinity form able to bind integrins.

Example 16 M4.1 Recognizes Unreduced Human TEM-1 but not Murine TEM-1

CHO-TEM-1 cells, mouse 2H11 cells, parental CHO-K1 cells, mouse NS0cells, and mouse MS1 cells were cultured in complete RPMI1640 (RPMI1640;sodium pyruvate; nonessential amino acids; L-glutamine, and FBS;Invitrogen Corp.). Human primary pericytes were cultured in PerciyteMedium (500 ml of basal medium (Cat #1201), 10 ml (2%) of fetal bovineserum (FBS, Cat. No. 0025), 5 ml of pericyte growth supplement (PGS,Cat. No. 1252) and 5 ml of penicillin/streptomycin solution (P/S, Cat.No. 0503); Invitrogen Corp.). Cells were grown at 37° C. and 5% CO₂ in ahumidified incubator. Cells were deadhered with TrypLE™ Select(Invitrogen Corp., catalog no. 12563-011), washed, and counted. Cellswere lysed at 2×10⁷ cells in RIPA Lysis buffer containing proteaseinhibitors and incubated on ice for 10 minutes. Insoluble material waspelleted at 10,000×G for 10 minutes at 4° C., and supernatants weretransferred to fresh tubes. Aliquots were mixed with an equal volume of2× protein loading buffer with or without 10% 2-mercaptoethanol(reducing agent). 15 μL (1.5×10⁵ cells) of lysate were loaded onto a 15well 4-12% Bis/Tris SDS-PAGE gel and electrophoresed for 30 minutes at200V in MES running buffer. The gel was electroblotted onto PVDF, thenblocked for 1 hour at room temperature with rocking in 5% milk-TBST (5%M-TBST). M4.1 blots were probed with M4.1 in 5% M-TBST at 3.3 ug/mLovernight at 4° C.

Rabbit anti-tem-1 polyclonal antibody blots were probed with a 1:300dilution (4.5 mg/ml stock Lot #: NB487-76) of antibody in 5% M-TBSTovernight at 4° C. Antibody M4.1, like antibody M4, is a humanizedantibody to human endosialin. Membranes were washed 5 times for 5minutes each with 30 mL TBST at room temperature. HRP-conjugated goatanti-human IgG (H+L) (Jackson Immuno, 1 mg/mL stock) was diluted1:20,000 in 5% M-TBST as a secondary antibody for probing the M4.1 blotsfor 30 minutes at room temperature. HRP-conjugated goat anti-rabbit(H+L) secondary antibody was used to blot the polyclonal anti-TEM-1blots for 30 minutes at room temperature. Membranes were washed 5 timesfor 5 minutes each with 30 mL TBST at room temperature. Signal wasdetected by chemiluminescence using the Femto Western Blot DetectionSystem (Pierce) as per manual.

As illustrated in FIG. 15, M4.1 recognizes unreduced human TEM-1 inCHO-TEM-1 cells and human primary pericytes but not murine TEM-1 (SEQ IDNO:2) in mouse 2H11 cells (FIG. 15). Rabbit polyclonal against humanTEM-1 (rabPAb TEM-1) recognizes human TEM-1 in CHO-TEM-1 cells and humanpericytes, but also murine TEM-1 in mouse 2H11 cells. Neither M4.1 norrabPAb TEM-1 reacted against lysates from parental CHO-K1 cells or mouseNS0 and MS1 cells due to lack of TEM-1 expression in these cells. OnlyrabPAb TEM-1 reacted with reduced human TEM-1, albeit to a lesser extentwhen compared to unreduced TEM-1.

The present invention is not limited to the embodiments described andexemplified above, but is capable of variation and modification withinthe scope of the appended claims.

What is claimed:
 1. A method for inhibiting the interaction of anendosialin-expressing cell with collagen or fibronectin, comprisingcontacting said endosialin-expressing cell with an antibody produced bycells having ATCC Access. No. PTA-9017, wherein binding of said antibodyto endosialin expressed on the surface of the endosialin-expressing cellinhibits the interaction of said endosialin-expressing cell with saidcollagen or fibronectin.
 2. The method of claim 1, wherein inhibitingthe interaction of said endosialin-expressing cell with said collagen orfibronectin inhibits migration of the endosialin-expressing cell.
 3. Themethod of claim 1, wherein inhibiting the interaction of saidendosialin-expressing cell with said collagen or fibronectin inhibitsthe activation of a matrix metalloprotease.
 4. The method of claim 3wherein the matrix metalloprotease is MMP-9.
 5. The method of claim 1,wherein inhibiting the interaction of said endosialin-expressing cellwith said collagen or fibronectin inhibits the expression of a matrixmetalloprotease.
 6. The method of claim 5 wherein the matrixmetalloprotease is MMP-9.
 7. The method of claim 1 wherein inhibitingthe interaction of said endosialin-expressing cell with said collagen orfibronectin inhibits the activation of integrin β1, β2, or β3.
 8. Themethod of claim 1 wherein said endosialin-expressing cell is a mammaliancell.
 9. The method of claim 1, wherein said endosialin-expressing cellis a neoplastic cell.
 10. A method for inhibiting neovascularization ina subject comprising administering to the subject a therapeuticallyeffective amount of an antibody produced by cells having ATCC Access.No. PTA-9017, wherein said antibody inhibits the interaction ofendosialin expressed on the surface of a cell with collagen orfibronectin, and wherein inhibiting said interaction of endosialinexpressed on the surface of said cell with said collagen or fibronectininhibits neovascularization of a tissue, organ, or neoplasm in thesubject.
 11. The method of claim 10, wherein inhibiting said interactionof endosialin expressed on the surface of said cell with said collagenor fibronectin inhibits migration of the cell.
 12. The method of claim10, wherein inhibiting said interaction of endosialin expressed on thesurface of said cell with said collagen or fibronectin inhibits theactivation of a matrix metalloprotease.
 13. The method of claim 12,wherein the matrix metalloprotease is MMP-9.
 14. The method of claim 10,wherein inhibiting said interaction of endosialin expressed on thesurface of said cell with said collagen or fibronectin inhibits theexpression of a matrix metalloprotease.
 15. The method of claim 14,wherein the matrix metalloprotease is MMP-9.
 16. The method of claim 10,wherein inhibiting said interaction of endosialin expressed on thesurface of said cell with said collagen or fibronectin inhibits theactivation of integrin β1, β2, or β3.
 17. The method of claim 10,wherein said cell is a mammalian cell.
 18. The method of claim 10,wherein said cell is a neoplastic cell.
 19. A method for inhibitingangiogenesis in a subject comprising administering to the subject atherapeutically effective amount of an antibody produced by cells havingATCC Access. No. PTA-9017, wherein said antibody inhibits theinteraction of endosialin expressed on the surface of a cell withcollagen or fibronectin, and wherein inhibiting said interaction ofendosialin expressed on the surface of said cell with said collagen orfibronectin inhibits angiogenesis of a tissue, organ, or neoplasm in thesubject.
 20. The method of claim 19, wherein inhibiting said interactionof endosialin expressed on the surface of said cell with said collagenor fibronectin inhibits migration of the cell.
 21. The method of claim19, wherein inhibiting said interaction of endosialin expressed on thesurface of said cell with said collagen or fibronectin inhibits theactivation of a matrix metalloprotease.
 22. The method of claim 21,wherein the matrix metalloprotease is MMP-9.
 23. The method of claim 19,wherein inhibiting said interaction of endosialin expressed on thesurface of said cell with said collagen or fibronectin inhibits theexpression of a matrix metalloprotease.
 24. The method of claim 23,wherein the matrix metalloprotease is MMP-9.
 25. The method of claim 19,wherein inhibiting said interaction of endosialin expressed on thesurface of said cell with said collagen or fibronectin inhibits theactivation of integrin β1, β2, or β3.
 26. The method of claim 19,wherein said cell is a mammalian cell.
 27. The method of claim 19,wherein said cell is a neoplastic cell.
 28. A method for inhibiting theinteraction of an endosialin-expressing cell with collagen orfibronectin, comprising obstructing endosialin expressed on the surfaceof said cell, wherein said obstructing inhibits the interaction of saidcell with said collagen or fibronectin, wherein said obstructingcomprises contacting said cell with an antibody produced by cells havingATCC Access. No. PTA-9017.